From 0c0d1cf10f521654dd675619f7f51851542f8f87 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 22 Jan 2019 16:47:31 +0200 Subject: [PATCH 001/528] adding easyconfigs: Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb --- ...ree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb new file mode 100644 index 00000000000..560ec3fc001 --- /dev/null +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' +name = 'Embree' +version = "3.4.0" + +homepage = 'https://embree.github.io/' +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" + +toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.3.0'} + +source_urls = ['https://github.com/embree/embree/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [] + +builddependencies = [('CMake', '3.11.4')] + +dependencies = [ + ('ispc', '1.10.0'), + ('tbb', '2018.1.163'), +] + +configopts = '-DEMBREE_TUTORIALS=OFF ' + +moduleclass = 'vis' From 3a9544975460d9bc726c3e430326a396e19cc9df Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 24 Jan 2019 11:04:39 +0200 Subject: [PATCH 002/528] added checksum and changed to available easyconfig-dependencies --- ....4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..19f13449e6a --- /dev/null +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' +name = 'Embree' +version = '3.4.0' + +gccver = '6.4.0' +binutilsver = '2.28' +gccsuff = '-GCC-%s' % (gccver) + +homepage = 'https://embree.github.io/' +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" + +toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff,binutilsver)} + +source_urls = ['https://github.com/embree/embree/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] + +builddependencies = [('CMake', '3.11.4','-GCCcore-%s' % gccver),] + +dependencies = [ + ('ispc', '1.10.0'), + ('tbb', '2018_U5','-GCCcore-%s' % gccver), +] + +configopts = '-DEMBREE_TUTORIALS=OFF ' + +moduleclass = 'vis' From 1a849ed22a7fd032557b9f7c8cb9d2c8875e3f9c Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Thu, 24 Jan 2019 11:04:35 +0100 Subject: [PATCH 003/528] Delete Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb --- ...ree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb deleted file mode 100644 index 560ec3fc001..00000000000 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'CMakeMake' -name = 'Embree' -version = "3.4.0" - -homepage = 'https://embree.github.io/' -description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" - -toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.3.0'} - -source_urls = ['https://github.com/embree/embree/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = [] - -builddependencies = [('CMake', '3.11.4')] - -dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018.1.163'), -] - -configopts = '-DEMBREE_TUTORIALS=OFF ' - -moduleclass = 'vis' From 75800d4c3c8b677f43474e822ba32bd2df7c6325 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 15:36:42 +0100 Subject: [PATCH 004/528] Calcam v2.1.0 for Python/3.6.4-intel-2018a --- .../Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..10926635e02 --- /dev/null +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Calcam' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://euratom-software.github.io/calcam' + +description = """Calcam is a Python package providing tools for spatial calibration + of cameras, i.e. determining the mapping between pixel coordinates in an image and + real-world 3D sight lines & coordinates.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/euratom-software/calcam/archive'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': 'v%(version)s.tar.gz', # provided source tarball is not versioned... +}] +checksums = ['8348545719209650ac62ed8c77087ec6e42df77995ead59f3b2e035da962a679'] + +dependencies = [ + ('Python', '3.6.4'), + ('matplotlib', '2.1.2', '-Python-%(pyver)s'), + ('OpenCV', '3.4.1', '-Python-%(pyver)s'), + ('PyQt5', '5.9.2', '-Python-%(pyver)s'), + ('VTK', '8.1.0', '-Python-%(pyver)s'), +] + +download_dep_fail = True + +preinstallopts = 'echo n |' + +sanity_check_paths = { + 'files': ['bin/calcam'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From e76c2911c0844f1e522300bf237816b189477ca5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 18:36:47 +0100 Subject: [PATCH 005/528] Calcam v2.1.0 for Python/2.7.14-intel-2018a --- .../Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..2078324412c --- /dev/null +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Calcam' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://euratom-software.github.io/calcam' + +description = """Calcam is a Python package providing tools for spatial calibration + of cameras, i.e. determining the mapping between pixel coordinates in an image and + real-world 3D sight lines & coordinates.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/euratom-software/calcam/archive'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': 'v%(version)s.tar.gz', # provided source tarball is not versioned... +}] +checksums = ['8348545719209650ac62ed8c77087ec6e42df77995ead59f3b2e035da962a679'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.2', '-Python-%(pyver)s'), + ('OpenCV', '3.4.1', '-Python-%(pyver)s'), + ('PyQt5', '5.9.2', '-Python-%(pyver)s'), + ('VTK', '8.1.0', '-Python-%(pyver)s'), +] + +download_dep_fail = True + +preinstallopts = 'echo n |' + +sanity_check_paths = { + 'files': ['bin/calcam'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From d6904e810a1c2e7401890df79f727c382c6ce57d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 18:59:55 +0100 Subject: [PATCH 006/528] OpenCV v3.4.1 for Python/2.7.14 on intel/2018a --- .../OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..e017af4d366 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,46 @@ +name = 'OpenCV' +version = '3.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/dfe3162c237af211e98b8960018b564bc209261d/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_2017u3_lnx_intel64_general_20170822.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '24bda432eaace9e992322dcc3d30144cefa5314c2424d4aa02e5fe3fa9dd17bd', # 3.4.1.zip + # ippicv_2017u3_lnx_intel64_general_20170822.tgz + '9a4b14a24d31768c3ead0720f27d55dcf80723b5ba1cd8903bed1fd69f1b9e2e', +] + +builddependencies = [ + ('CMake', '3.10.2'), +] + +dependencies = [ + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.4.2'), + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8.0_162', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.54.3'), + ('GTK+', '2.24.32'), +] + +moduleclass = 'vis' From 9cc6d66fc553c667499223912ea213a7045fca9a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 19:01:39 +0100 Subject: [PATCH 007/528] PyQt5 v5.9.2 for Python/2.7.14 on intel/2018a --- .../PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..68fd5bf4ffd --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +checksums = ['c190dac598c97b0113ca5e7a37c71c623f02d1d713088addfacac4acfa4b8394'] + +dependencies = [ + ('Python', '2.7.14'), + ('SIP', '4.19.8', versionsuffix), + ('Qt5', '5.10.1'), +] + +configopts = "configure.py --confirm-license --verbose" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages --bindir=%(installdir)s/bin" +configopts += " --designer-plugindir=%(installdir)s/plugins/designer --qml-plugindir=%(installdir)s/plugins/PyQt5" +configopts += " --no-sip-files --no-stubs " + +options = {'modulename': '%(name)s'} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' From 6bcd154a657d90b272e588742df01afb61eb98d6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Jan 2019 08:39:24 +0100 Subject: [PATCH 008/528] SIP v4.19.8 for Python/2.7.14-intel-2018a --- .../SIP-4.19.8-intel-2018a-Python-2.7.14.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..35357ae851c --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7eaf7a2ea7d4d38a56dd6d2506574464bddf7cf284c960801679942377c297bc'] + +dependencies = [('Python', '2.7.14')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' From 3692b57052b981f9dcaec345b9dd36ce157ad744 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 2 Feb 2019 19:09:29 +0100 Subject: [PATCH 009/528] Use pip to install Calcam v2.1.0 with Python/2.7.14 and Python/3.6.4 --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 2 ++ .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index 2078324412c..d15eb614ace 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -27,6 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] +use_pip = True + download_dep_fail = True preinstallopts = 'echo n |' diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 10926635e02..78fed5ee963 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -27,6 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] +use_pip = True + download_dep_fail = True preinstallopts = 'echo n |' From cf6e06b286bc0ad30ccc6f2fe1e5a1a4656313bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 10:14:50 +0100 Subject: [PATCH 010/528] {bio}[intel/2018b] atropos v1.1.21 w/ Python 3.6.6 (+ deps) --- ...atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 78 +++++++++++++++++++ .../NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb | 40 ++++++++++ .../NGS-2.9.3_fix-python-install-prefix.patch | 13 ++++ .../Pysam-0.15.1-intel-2018b-Python-3.6.6.eb | 38 +++++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..440192d5efc --- /dev/null +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'atropos' +version = '1.1.21' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://atropos.readthedocs.io' +description = "Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. " + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), + ('pytest', '3.8.2', versionsuffix), + ('NGS', '2.9.3', versionsuffix), # required for srastream +] + +#use_pip = True + +exts_list = [ + ('python-utils', '2.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-utils/'], + 'checksums': ['34aaf26b39b0b86628008f2ae0ac001b30e7986a8d303b61e1357dfcdad4f6d3'], + }), + ('progressbar2', '3.39.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar2/'], + 'checksums': ['6eb5135b987caca4212d2c7abc2923d4ad5ba18bb34ccbe7044b3628f52efc2c'], + 'modulename': 'progressbar', + }), + ('tqdm', '4.31.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], + 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], + }), + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file/'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('screed', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/screed/'], + 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], + }), + ('khmer', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/khmer/'], + 'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'], + }), + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('pokrok', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pokrok'], + 'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'], + }), + ('xphyle', '4.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xphyle/'], + 'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'], + }), + ('srastream', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/srastream/'], + 'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/a/atropos/'], + 'checksums': ['8178af467734b299960edae15d8835a2228ba0cc1b718af436c7d86041fbd4ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/atropos'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..410071ff7cb --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['NGS-%(version)s_fix-python-install-prefix.patch'] +checksums = [ + 'd16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d', # 2.9.3.tar.gz + '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', # NGS-2.9.3_fix-python-install-prefix.patch +] + +dependencies = [('Python', '3.6.6')] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-python' + +installopts = "-C ngs-sdk && make install -C ngs-python" + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib64/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-adapt-c++.a', 'lib64/libngs-c++.a'], + 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch b/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch new file mode 100644 index 00000000000..92b99ee5e44 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch @@ -0,0 +1,13 @@ +fix installation prefix for installing NGS Python bindings +author: Kenneth Hoste (HPC-UGent) +--- ngs-2.9.3/ngs-python/Makefile.python.orig 2019-02-12 09:33:55.145471383 +0100 ++++ ngs-2.9.3/ngs-python/Makefile.python 2019-02-12 09:34:09.145729890 +0100 +@@ -85,7 +85,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..d8ccf82a7a9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.15.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed'] + +dependencies = [ + ('Python', '3.6.6'), + ('ncurses', '6.1'), + ('cURL', '7.60.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 9db07ad6cfc3cf2cae72a71065f6be2fe71611c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 11:40:58 +0100 Subject: [PATCH 011/528] use pip to install atropos --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 440192d5efc..487026ab37c 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ dependencies = [ ('NGS', '2.9.3', versionsuffix), # required for srastream ] -#use_pip = True +use_pip = True exts_list = [ ('python-utils', '2.3.0', { From 9ef18507280d8b6168c643a97fca0d1cde8f1e8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 10:47:56 +0100 Subject: [PATCH 012/528] adding easyconfigs: CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb, SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb --- .../CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 45 +++++++++++++++++++ ...iteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb | 22 +++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f3d00fec42d --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'CVXOPT' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'ea62a2a1b8e2db3a6ae44ac394f58e4620149af226c250c6f2b18739b48cfc21', # cvxopt-1.2.3.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('GSL', '2.5'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +postinstallcmds = ['nosetests'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb new file mode 100644 index 00000000000..7b5db09357a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb @@ -0,0 +1,22 @@ +name = 'SuiteSparse' +version = '5.1.2' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4ec8d344bd8e95b898132ddffd7ee93bfbb2c1224925d11bab844b08f9b4c3b7'] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " + +moduleclass = 'numlib' From 92c07fa70c3c48731574c78a79d4b66226c7aadd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 11:00:53 +0100 Subject: [PATCH 013/528] allow different dep variants for NGS (different language bindings) --- test/easyconfigs/easyconfigs.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..2184e800ecf 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -175,6 +175,8 @@ def check_dep_vars(dep, dep_vars): # 'guilty' until proven 'innocent' res = False + version_regex = re.compile('^version: (?P[^;]+);') + # filter out binutils with empty versionsuffix which is used to build toolchain compiler if dep == 'binutils' and len(dep_vars) > 1: empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] @@ -185,10 +187,17 @@ def check_dep_vars(dep, dep_vars): elif dep == 'HTSlib' and len(dep_vars) > 1: for key, ecs in dep_vars.items(): # filter out HTSlib variants that are only used as dependency for BCFtools with same version - htslib_ver = re.search('^version: (?P[^;]+);', key).group('ver') + htslib_ver = version_regex.search(key).group('version') if all(ec.startswith('BCFtools-%s-' % htslib_ver) for ec in ecs): dep_vars.pop(key) + # multiple variants of NGS is OK, as long as they only differ by versionsuffix (same version) + # to allow for different language bindings (Java, Python 2, Python 3, ...) + elif dep == 'NGS' and len(dep_vars) > 1: + ngs_vers = [version_regex.search(key).group('version') for key in dep_vars] + if len(ngs_vers) == 1: + dep_vars.pop(key) + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains elif dep in ['FFTW', 'imkl']: serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] @@ -199,7 +208,7 @@ def check_dep_vars(dep, dep_vars): # as long as that's indicated by the versionsuffix elif dep in ['Boost', 'R'] and len(dep_vars) > 1: for key in dep_vars.keys(): - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') # filter out dep version if all easyconfig filenames using it include specific dep version if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): dep_vars.pop(key) From 7684c08c7ccfeffe7be0500a4288022db5cffe50 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 12 Mar 2019 09:57:00 +0200 Subject: [PATCH 014/528] update --- ....4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 10 +++---- easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 27 +++++++++++++++++++ 2 files changed, 32 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 19f13449e6a..9ba7175fd0d 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' name = 'Embree' -version = '3.4.0' +version = "3.4.0" gccver = '6.4.0' binutilsver = '2.28' @@ -9,17 +9,17 @@ gccsuff = '-GCC-%s' % (gccver) homepage = 'https://embree.github.io/' description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" -toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff,binutilsver)} +toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} source_urls = ['https://github.com/embree/embree/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] -builddependencies = [('CMake', '3.11.4','-GCCcore-%s' % gccver),] +builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018_U5','-GCCcore-%s' % gccver), + ('ispc', '1.10.0'), + ('tbb', '2018_U5', '-GCCcore-%s' % gccver), ] configopts = '-DEMBREE_TUTORIALS=OFF ' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb new file mode 100644 index 00000000000..82c7a63390c --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'ispc' +version = '1.10.0' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for 'single program, multiple data' (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] +checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3'] + +sanity_check_paths = { + 'files': ["bin/ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' From 28d3bcf046b234a39590bd013a6b89433ed982e3 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 12 Mar 2019 12:39:00 +0200 Subject: [PATCH 015/528] update --- .../Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 9ba7175fd0d..76d37e5201a 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -18,8 +18,8 @@ checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018_U5', '-GCCcore-%s' % gccver), + ('ispc', '1.10.0', '', True), + ('tbb', '2018_U5', '', ('GCCcore', gccver)), ] configopts = '-DEMBREE_TUTORIALS=OFF ' From 2ad87f5cb39e8b3405a92bb46ed57e4f26f1cf4a Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Tue, 12 Mar 2019 15:47:08 +0100 Subject: [PATCH 016/528] Update Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb Rearrange description --- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 76d37e5201a..8d9da0f977c 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -7,7 +7,13 @@ binutilsver = '2.28' gccsuff = '-GCC-%s' % (gccver) homepage = 'https://embree.github.io/' -description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. +The target users of Intel® Embree are graphics application engineers who want to improve the performance of +their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. +The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. +Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches +the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit +from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} From ec74e6b46d1292d693f70d8ba2c17280edcba7c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 22 Mar 2019 14:01:48 +0100 Subject: [PATCH 017/528] update homepage and source_urls --- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 47d9f67b516..6c83c0b51ab 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = 'GLIMMER' version = '3.02b' -homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index 8e1a574fde6..a8932d6d6a3 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -12,13 +12,13 @@ easyblock = 'MakeCp' name = 'GLIMMER' version = '3.02b' -homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.cbcb.umd.edu/software/%(namelower)s'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] checksums = ['a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3'] diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 9224bccf7f9..7b9af0a1d22 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://www.cbcb.umd.edu/software/glimmer/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index 90a24de0cf2..e7f8082104e 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://www.cbcb.umd.edu/software/glimmer/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' From 5d2be2c1dd8adb8f26fc7c18e9e59579518b5876 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 22 Mar 2019 20:47:35 +0100 Subject: [PATCH 018/528] Add checksums --- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 1 + easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 2 +- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 1 + 4 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 6c83c0b51ab..59dcbaec249 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index a8932d6d6a3..1c389bd393d 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] -checksums = ['a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3'] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = "-C ./src" diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 7b9af0a1d22..da9c09fd6d5 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index e7f8082104e..49bd7675820 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' From a5d711adf8dc1aea92b6b98564650d69fae9f6fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 9 May 2019 18:17:40 +0200 Subject: [PATCH 019/528] Improve comments in Calcam v2.1.0 EB files regarding use of preinstallopts --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 2 ++ .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index d15eb614ace..ba8db2d6ade 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -31,6 +31,8 @@ use_pip = True download_dep_fail = True +# Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. +# The following line answers "n" to this question and skips the conversion. preinstallopts = 'echo n |' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 78fed5ee963..193dc5501b8 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -31,6 +31,8 @@ use_pip = True download_dep_fail = True +# Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. +# The following line answers "n" to this question and skips the conversion. preinstallopts = 'echo n |' sanity_check_paths = { From 09a97924af2a6cb48bed44f43d27a87c24c1659f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 25 Sep 2019 10:01:58 +0200 Subject: [PATCH 020/528] added ragoo easyconfig and deps --- ...ervaltree-3.0.2-foss-2018b-Python-3.6.6.eb | 30 ++++++++++++++++ .../m/minimap2/minimap2-2.17-foss-2018b.eb | 34 ++++++++++++++++++ .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb create mode 100644 easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ca15abe5443 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'intervaltree' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = 'A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment' + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/chaimleib/intervaltree/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e8ab75b66077f2e5fb85ac56cb6df834689edb048d38601d53d8867cce3b77d1'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/intervaltree-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb new file mode 100644 index 00000000000..59e42b8bb3f --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = "2.17" + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] + +files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a76297e3b5a --- /dev/null +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "PythonPackage" + +name = 'RaGOO' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/malonge/RaGOO' +description = 'A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome' + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/malonge/RaGOO/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] + +dependencies = [ + ('Python', '3.6.6'), + ('minimap2', '2.17'), + ('intervaltree', '3.0.2', '-Python-%(pyver)s'), + # numpy dependency is provided by the python module +] + +sanity_check_paths = { + 'files': ['bin/ragoo.py'], + 'dirs': [], +} + +# workaround for the python sanity check trying to do 'import ragoo' +options = {'modulename': 'os'} + +moduleclass = 'bio' From e3ec482a382aba8e58955b0ac2600739ff4626e3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 1 Jun 2020 15:54:29 +0200 Subject: [PATCH 021/528] adding easyconfigs: numba-0.49.1-foss-2020a-Python-3.8.2.eb, LLVM-8.0.1-GCCcore-9.3.0.eb --- .../l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb | 45 +++++++++++++++++ .../numba-0.49.1-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b39d56ac18c --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '8.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['44787a6d02f7140f145e2250d56c9f849334e11f9ae379827510ed72f12b75e7'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Python', '3.8.2'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ea12473895c --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.49.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('LLVM', '8.0.1'), +] + +use_pip = True + +exts_list = [ + ('llvmlite', '0.32.1', { + 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'checksums': [ + '41262a47b8cbba5a09203b15b65fbdf11192f92aa226c81e99115acdee8f3b8d', # llvmlite-0.32.1.tar.gz + # llvmlite-0.30.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['89e1ad8215918036b0ffc53501888d44ed44c1f2cb09a9e047d06af5cd7e7a5a'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From 48530e8525d8af4f30de98d47adfdce1f79a1d07 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 6 Jul 2020 18:03:54 +0200 Subject: [PATCH 022/528] Code Saturne from JSC --- .../Code_Saturne-6.1.1-gpsmkl-2019a.1.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb diff --git a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb new file mode 100644 index 00000000000..53c5c098a0b --- /dev/null +++ b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb @@ -0,0 +1,56 @@ +# easyconfig file for Code_Saturne +# author: Metin Cakircali (Juelich Supercomputing Centre) +name = 'Code_Saturne' +version = '6.1.1' + +# extra option for the SLURM batch system +slurm = True + +homepage = 'https://www.code-saturne.org' +description = """Code_Saturne solves the Navier-Stokes equations +for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, +laminar or turbulent, incompressible or weakly dilatable, +isothermal or not, with scalars transport if required. + +Code_Saturne %(version)s%(versionsuffix)s is installed in +$EBROOTCODE_SATURNE +""" +site_contacts = 'a.strube@fz-juelich.de' + +toolchain = {'name': 'gpsmkl', 'version': '2019a.1'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +sources = [{ + 'source_urls': ['https://github.com/code-saturne/code_saturne/archive/'], + 'filename': 'v%(version)s.tar.gz' +}] + +builddependencies = [ + ('Autotools', '20180311'), + ('gettext', '0.19.8.1'), + ('Bison', '3.3.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('Python', '3.6.8'), + ('PyQt5', '5.11.3', '-Python-%(pyver)s'), + ('HDF5', '1.10.5'), + ('MED', '4.0.0'), + ('CGNS', '4.1.1'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.0.6'), + ('ParaView', '5.6.0', '-Python-%(pyver)s', ('gpsmkl', '2019a.1')), +] + +# better to configure these dependents explicitly +configopts = ['--with-med=$EBROOTMED --with-cgns=$EBROOTCGNS \ + --with-metis=$EBROOTPARMETIS --with-scotch=$EBROOTSCOTCH'] + +parallel = 48 + +modloadmsg = "To benefit from shell completion for %(name)s commands and\n" +modloadmsg += "options, you may also source a bash completion file by;\n" +modloadmsg += ". $CS_BASH\n" + +moduleclass = 'cae' From 7442860a6727cf365816520e6501fdf31dc3f205 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Jul 2020 18:30:05 +0200 Subject: [PATCH 023/528] numba v0.50.0 with LLVM v9.0.1 for foss/2020a --- .../l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb | 45 ------------------- ...> numba-0.50.0-foss-2020a-Python-3.8.2.eb} | 10 ++--- 2 files changed, 5 insertions(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb rename easybuild/easyconfigs/n/numba/{numba-0.49.1-foss-2020a-Python-3.8.2.eb => numba-0.50.0-foss-2020a-Python-3.8.2.eb} (82%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index b39d56ac18c..00000000000 --- a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'LLVM' -version = '8.0.1' - -homepage = "https://llvm.org/" -description = """The LLVM Core libraries provide a modern source- and target-independent - optimizer, along with code generation support for many popular CPUs - (as well as some less common ones!) These libraries are built around a well - specified code representation known as the LLVM intermediate representation - ("LLVM IR"). The LLVM Core libraries are well documented, and it is - particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'gnu++11'} - -source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] -sources = ['llvm-%(version)s.src.tar.xz'] -checksums = ['44787a6d02f7140f145e2250d56c9f849334e11f9ae379827510ed72f12b75e7'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), -] - -configopts = '-DBUILD_SHARED_LIBS=ON ' -# required to install extra tools in bin/ -configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' - -sanity_check_paths = { - 'files': ['bin/llvm-ar', 'bin/FileCheck'], - 'dirs': ['include/llvm', 'include/llvm-c'], -} - -separate_build_dir = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb similarity index 82% rename from easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb index ea12473895c..0ee44b6c216 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'numba' -version = '0.49.1' +version = '0.50.0' versionsuffix = '-Python-%(pyver)s' homepage = 'https://numba.pydata.org/' @@ -17,24 +17,24 @@ toolchainopts = {'pic': True} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '8.0.1'), + ('LLVM', '9.0.1'), ] use_pip = True exts_list = [ - ('llvmlite', '0.32.1', { + ('llvmlite', '0.33.0', { 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ - '41262a47b8cbba5a09203b15b65fbdf11192f92aa226c81e99115acdee8f3b8d', # llvmlite-0.32.1.tar.gz + '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', # llvmlite-0.33.0.tar.gz # llvmlite-0.30.0_fix-ffi-Makefile.patch '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', ], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - 'checksums': ['89e1ad8215918036b0ffc53501888d44ed44c1f2cb09a9e047d06af5cd7e7a5a'], + 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], }), ] From 741f5ccbdf0ad67a8ae4cda4ea30ec7730eb5a7b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 16 Jul 2020 21:27:40 +0200 Subject: [PATCH 024/528] numba v0.50.1 for foss/2020a and Python/3.8.2 --- ...ython-3.8.2.eb => numba-0.50.1-foss-2020a-Python-3.8.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/numba/{numba-0.50.0-foss-2020a-Python-3.8.2.eb => numba-0.50.1-foss-2020a-Python-3.8.2.eb} (92%) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb similarity index 92% rename from easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index 0ee44b6c216..13cfcdf1e7f 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'numba' -version = '0.50.0' +version = '0.50.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://numba.pydata.org/' @@ -34,7 +34,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], + 'checksums': ['89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7'], }), ] From 46da040cf547a7621339063981d29d48d4c2b0bf Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 17 Jul 2020 11:43:31 +0200 Subject: [PATCH 025/528] numba v0.50.1 for foss/2020a and Python/3.8.2: Add sanity_pip_check --- .../easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index 13cfcdf1e7f..e5b096d734b 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('llvmlite', '0.33.0', { From 25114bd3453a65affac4efe21775cca22860c862 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 11 Dec 2020 12:36:23 +1050 Subject: [PATCH 026/528] adding easyconfigs: ANGEL-3.0-foss-2019a-Python-3.7.2.eb --- .../ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..23a199adbb3 --- /dev/null +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'ANGEL' +version = '3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/PacificBiosciences/ANGEL' +description = """ANGEL: Robust Open Reading Frame prediction""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PacificBiosciences/ANGEL/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0319553055d3dfc84a4f732ed246c180c23ee9c397810c96acd7940721ae57d'] + +dependencies = [ + ('Python', '3.7.2'), + ('Biopython', '1.73'), + ('scikit-learn', '0.20.3'), +] + +bin_files = [ + 'dumb_predict.py', + 'angel_make_training_set.py', + 'angel_train.py', + 'angel_predict.py', + 'angel_compare_files.py', +] + +skipsteps = ['sanitycheck'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in bin_files], + 'dirs': [''], +} + +moduleclass = 'bio' From e66edaf1e0c4480a96f22014d9d339c83a99bcaa Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 11 Dec 2020 14:40:31 +1050 Subject: [PATCH 027/528] local var sync --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 23a199adbb3..8cdb56bc1c7 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ] -bin_files = [ +local_bin_files = [ 'dumb_predict.py', 'angel_make_training_set.py', 'angel_train.py', @@ -41,7 +41,7 @@ bin_files = [ skipsteps = ['sanitycheck'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in bin_files], + 'files': ['bin/%s' % x for x in local_bin_files], 'dirs': [''], } From 10d3980b1438c5edc3825ed14b18e7162bfed917 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 17 Dec 2020 10:24:19 +1050 Subject: [PATCH 028/528] sanity_check + --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 8cdb56bc1c7..37a86c26221 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -35,10 +35,10 @@ local_bin_files = [ 'angel_make_training_set.py', 'angel_train.py', 'angel_predict.py', - 'angel_compare_files.py', + 'angel_compare_files.py' ] -skipsteps = ['sanitycheck'] +options = {'modulename': False} sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bin_files], From 7d3b6fddf0b98de7189ac66761b880fe8a894eb6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 17 Dec 2020 10:46:37 +1050 Subject: [PATCH 029/528] prereqs + --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 37a86c26221..7bb4ef20c12 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -30,6 +30,10 @@ dependencies = [ ('scikit-learn', '0.20.3'), ] +download_dep_fail = True + +use_pip = False + local_bin_files = [ 'dumb_predict.py', 'angel_make_training_set.py', From 7b36bca7fbe01e5afff3d96be79e8ca6c97c44d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Jan 2021 14:23:00 +0100 Subject: [PATCH 030/528] enable use_pip and sanity_pip_check in ANGEL easyconfig --- .../a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 7bb4ef20c12..2c7340a7bec 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -31,8 +31,7 @@ dependencies = [ ] download_dep_fail = True - -use_pip = False +use_pip = True local_bin_files = [ 'dumb_predict.py', @@ -46,7 +45,9 @@ options = {'modulename': False} sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bin_files], - 'dirs': [''], + 'dirs': [], } +sanity_pip_check = True + moduleclass = 'bio' From 9793c8e9df09ed10f3be7098016fc2990b69a0cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 18:37:35 +0100 Subject: [PATCH 031/528] adding easyconfigs: SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb and patches: SqueezeMeta-1.0.0_fix-hardcoding.patch --- ...eezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 82 +++++++++++++++++++ .../SqueezeMeta-1.0.0_fix-hardcoding.patch | 63 ++++++++++++++ 2 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..700c3b31af3 --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,82 @@ +easyblock = 'Tarball' + +name = 'SqueezeMeta' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jtamames/SqueezeMeta' +description = """SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, + covering all steps of the analysis.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/jtamames/SqueezeMeta/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SqueezeMeta-%(version)s_fix-hardcoding.patch'] +checksums = [ + '35fa45246fa3580e7ab00644176f719151465aa0ed5f0023d30075668baefb11', # v1.0.0.tar.gz + '5fe6b721669d022a1d891472d64061f217791ff8efd1642d34a03de18a21d677', # SqueezeMeta-1.0.0_fix-hardcoding.patch +] + +dependencies = [ + ('Perl', '5.28.0'), # provides XML::Parser + ('XML-LibXML', '2.0132', '-Perl-%(perlver)s'), + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('R', '3.5.1', versionsuffix), + ('BLAST+', '2.7.1'), + ('BWA', '0.7.17'), + #('barrnap', '0.9'), + ('CD-HIT', '4.6.8'), + ('CheckM', '1.0.13', versionsuffix), + ('DAS_Tool', '1.1.1', '-R-%(rver)s-Python-%(pyver)s'), # depends on prodigal & pullseq + ('DIAMOND', '0.9.22'), + ('MEGAHIT', '1.1.4', versionsuffix), + ('minimap2', '2.13'), + ('Java', '1.8', '', True), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('MetaBAT', '2.12.1', versionsuffix), + ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('AMOS', '3.1.0'), + ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), + ('SPAdes', '3.13.0'), + ('Bowtie2', '2.3.4.2'), + ('canu', '1.8', '-Perl-%(perlver)s'), + ('HMMER', '3.2.1'), + ('MUMmer', '4.0.0beta2'), + ('pplacer', '1.1.alpha19', '', True), + ('Short-Pair', '20170125', versionsuffix), + ('SAMtools', '1.9'), + ('CompareM', '0.0.23', versionsuffix), +] + +keepsymlinks = True + +postinstallcmds = [ + # backup patched barrnap + "cp %(installdir)s/bin/barrnap %(builddir)s/", + # remove vendored tools that are include as dependencies + "rm -r %(installdir)s/bin/*", + "cp %(builddir)s/barrnap %(installdir)s/bin/", + # fix shebang in Perl scripts + "sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/scripts/*.pl", + # also install SQMtools R library + "mkdir %(installdir)s/R && R CMD INSTALL lib/SQMtools --library=%(installdir)s/R/ --no-clean-on-error", +] + +sanity_check_paths = { + 'files': ['scripts/SqueezeMeta.pl'], + 'dirs': ['scripts/preparing_databases'], +} + +sanity_check_commands = ["""echo 'library("SQMtools")' | R -q --no-save"""] + +modextrapaths = { + 'PATH': 'scripts', + 'R_LIBS': 'R', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch new file mode 100644 index 00000000000..eb762a4a11a --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch @@ -0,0 +1,63 @@ +fix hardcoded paths, rely on specified dependencies via $PATH and $EBROOT* +author: Kenneth Hoste (HPC-UGent) +--- SqueezeMeta-1.0.0/scripts/SqueezeMeta_conf_original.pl.orig 2019-11-26 11:48:35.838688703 +0100 ++++ SqueezeMeta-1.0.0/scripts/SqueezeMeta_conf_original.pl 2019-11-26 11:52:57.253843644 +0100 +@@ -80,25 +80,25 @@ + + #-- External software + +-$metabat_soft="$installpath/bin/metabat2"; +-$maxbin_soft="$installpath/bin/MaxBin/run_MaxBin.pl"; +-$spades_soft="$installpath/bin/SPAdes/spades.py"; +-$barrnap_soft="$installpath/bin/barrnap"; +-$rdpclassifier_soft="java -jar $installpath/bin/classifier.jar"; +-$bowtie2_build_soft="$installpath/bin/bowtie2/bowtie2-build"; +-$bowtie2_x_soft="$installpath/bin/bowtie2/bowtie2"; +-$bwa_soft = "$installpath/bin/bwa"; +-$minimap2_soft = "$installpath/bin/minimap2"; +-$diamond_soft="$installpath/bin/diamond"; +-$hmmer_soft="$installpath/bin/hmmer/hmmsearch"; +-$megahit_soft="$installpath/bin/megahit/megahit"; +-$prinseq_soft="$installpath/bin/prinseq-lite.pl"; +-$prodigal_soft="$installpath/bin/prodigal"; +-$cdhit_soft="$installpath/bin/cd-hit-est"; +-$toamos_soft="$installpath/bin/AMOS/toAmos"; +-$minimus2_soft="$installpath/bin/AMOS/minimus2"; +-$checkm_soft="$installpath/bin/checkm"; +-$minpath_soft="python $installpath/bin/MinPath1.4.py"; +-$canu_soft="$installpath/bin/canu/canu"; +-$trimmomatic_soft="java -jar $installpath/bin/trimmomatic-0.38.jar"; +-$dastool_soft="$installpath/bin/DAS_Tool/DAS_Tool"; ++$metabat_soft="metabat2"; ++$maxbin_soft="$ENV{'EBROOTMAXBIN'}/run_MaxBin.pl"; ++$spades_soft="spades.py"; ++$barrnap_soft="barrnap"; ++$rdpclassifier_soft="java -jar $ENV{'EBROOTRDPMINCLASSIFIER'}/dist/classifier.jar"; ++$bowtie2_build_soft="bowtie2-build"; ++$bowtie2_x_soft="bowtie2"; ++$bwa_soft = "bwa"; ++$minimap2_soft = "minimap2"; ++$diamond_soft="diamond"; ++$hmmer_soft="hmmsearch"; ++$megahit_soft="megahit"; ++$prinseq_soft="prinseq-lite.pl"; ++$prodigal_soft="prodigal"; ++$cdhit_soft="cd-hit-est"; ++$toamos_soft="AMOS/toAmos"; ++$minimus2_soft="AMOS/minimus2"; ++$checkm_soft="checkm"; ++$minpath_soft="MinPath$ENV{'EBVERSIONMINPATH'}.py"; ++$canu_soft="canu"; +++$trimmomatic_soft="java -jar $ENV{'EBROOTTRIMMOMATIC'}/trimmomatic-$ENV{'EBVERSIONTRIMMOMATIC'}.jar"; +++$dastool_soft="DAS_Tool"; +--- SqueezeMeta-1.0.0/utils/sqm_hmm_reads.pl.orig 2019-11-26 11:53:35.804013957 +0100 ++++ SqueezeMeta-1.0.0/utils/sqm_hmm_reads.pl 2019-11-26 11:54:08.748159508 +0100 +@@ -15,7 +15,7 @@ + + use File::Basename; + my $utilsdir = dirname(__FILE__); +-my $shortpair_soft = "$utilsdir/../bin/Short-Pair/Short-Pair.py"; ++my $shortpair_soft = "Short-Pair.py"; + + my($numthreads,$pair1,$pair2,$pfam,$outfile,$dietext,$tempfile1,$tempfile2,$hel); + From 689e7650e05b9ca7e5e56c475d48a0082d4dc576 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 15:50:29 -0700 Subject: [PATCH 032/528] {devel}[foss/2020b] Spark 3.1.1 --- .../s/Spark/Spark-3.1.1-foss-2020b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb new file mode 100644 index 00000000000..ba34f767b68 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -0,0 +1,53 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.1.1' + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', True), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.2', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 0c4a3876d978c63d07a40cce30f259edce464391 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 17:53:07 -0700 Subject: [PATCH 033/528] non Cuda foss Arrow --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb new file mode 100644 index 00000000000..e4c0d64a274 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '0.17.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'http://apache.belnet.be/arrow/arrow-%(version)s/', + 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', +] +sources = ['apache-arrow-%(version)s.tar.gz'] +patches = ['Arrow-0.16.0_fix-intel.patch'] +checksums = [ + 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz + '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), # for numpy + ('Boost', '1.74.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From a02f0bd8731b9cd803069abaee7fdfb4f058fbdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 13:43:16 +0200 Subject: [PATCH 034/528] adding easyconfigs: antiSMASH-5.2.0-foss-2020b.eb, GlimmerHMM-3.0.4c-GCC-10.2.0.eb, HMMER2-2.3.2-GCC-10.2.0.eb, MUSCLE-3.8.1551-GCC-10.2.0.eb and patches: antiSMASH-5.2.0_Biopython-1.78.patch --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 91 ++++ .../antiSMASH-5.2.0_Biopython-1.78.patch | 470 ++++++++++++++++++ .../GlimmerHMM-3.0.4c-GCC-10.2.0.eb | 45 ++ .../h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb | 27 + .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 30 ++ 5 files changed, 663 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb new file mode 100644 index 00000000000..57fe702e6cf --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '5.2.0' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('DIAMOND', '2.0.7'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.3.2'), + ('MUSCLE', '3.8.1551'), + ('BLAST+', '2.11.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '4.11.2', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': ['meme_%(version)s_2.tar.gz'], + 'checksums': ['377238c2a9dda64e01ffae8ecdbc1492c100df9b0f84132d50c1cf2f68921b22'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme_%(version)s', + 'buildopts': 'CFLAGS="$CFLAGS -std=gnu89 -DUNIX -D__USE_FIXED_PROTOTYPES__ -fcommon"', + }), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('helperlibs', '0.2.1', { + 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'modulename': 'pysvg', + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.6', { + 'modulename': 'BCBio.GFF', + 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + }), + ('pyScss', '1.3.7', { + 'modulename': 'scss', + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'source_tmpl': '%s.tar.gz' % '-'.join(version.split('.')), + 'patches': ['antiSMASH-%(version)s_Biopython-1.78.patch'], + 'checksums': [ + 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz + '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch new file mode 100644 index 00000000000..ab977c49987 --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch @@ -0,0 +1,470 @@ +see https://github.com/antismash/antismash/pull/310 + +From 94eaa1570bd7a2be9e24238234ccd33ab08270c2 Mon Sep 17 00:00:00 2001 +From: Simon Shaw +Date: Tue, 29 Sep 2020 17:01:37 +0200 +Subject: [PATCH 1/2] chore: handle biopython's removal of Alphabet in 1.78 and + update + +--- + antismash/common/record_processing.py | 24 ++------------ + antismash/common/secmet/features/region.py | 3 ++ + .../secmet/features/test/test_region.py | 5 ++- + antismash/common/secmet/record.py | 32 +++++++++++++++---- + .../secmet/test/test_circular_conversion.py | 11 ++++--- + antismash/common/secmet/test/test_secmet.py | 20 ++++++++++-- + antismash/common/serialiser.py | 15 +++------ + antismash/common/test/helpers.py | 4 +-- + .../common/test/test_record_processing.py | 17 ---------- + .../modules/pfam2go/test/test_pfam2go.py | 3 +- + antismash/modules/tta/test/test_tta.py | 3 +- + setup.py | 2 +- + 12 files changed, 67 insertions(+), 72 deletions(-) + +diff --git a/antismash/common/record_processing.py b/antismash/common/record_processing.py +index 0ab8ef89..489d2b95 100644 +--- a/antismash/common/record_processing.py ++++ b/antismash/common/record_processing.py +@@ -7,10 +7,9 @@ + import functools + import logging + import re +-from typing import Any, Callable, List, Set, Tuple, Union ++from typing import Any, Callable, List, Set, Tuple + import warnings + +-import Bio + from Bio.Seq import Seq, UnknownSeq + from Bio.SeqRecord import SeqRecord + from helperlibs.bio import seqio +@@ -97,7 +96,7 @@ def parse_input_sequence(filename: str, taxon: str = "bacteria", minimum_length: + raise AntismashInputError("all input records smaller than minimum length (%d)" % minimum_length) + + for record in records: +- if isinstance(record.seq.alphabet, Bio.Alphabet.ProteinAlphabet) or not is_nucl_seq(record.seq): ++ if not Record.is_nucleotide_sequence(record.seq): + raise AntismashInputError("protein records are not supported: %s" % record.id) + + # before conversion to secmet records, trim if required +@@ -356,8 +355,6 @@ def pre_process_sequences(sequences: List[Record], options: ConfigType, genefind + sequences = [sanitise_sequence(sequences[0])] + else: + sequences = parallel_function(sanitise_sequence, ([record] for record in sequences)) +- for sequence in sequences: +- sequence.seq.alphabet = Bio.Alphabet.generic_dna + + for record in sequences: + if record.skip or not record.seq: +@@ -413,7 +410,7 @@ def sanitise_sequence(record: Record) -> Record: + has_real_content = True + else: + sanitised.append("N") +- record.seq = Seq("".join(sanitised), alphabet=record.seq.alphabet) ++ record.seq = Seq("".join(sanitised)) + if not has_real_content: + record.skip = "contains no sequence" + return record +@@ -446,21 +443,6 @@ def trim_sequence(record: SeqRecord, start: int, end: int) -> SeqRecord: + return new + + +-def is_nucl_seq(sequence: Union[Seq, str]) -> bool: +- """ Determines if a sequence is a nucleotide sequence based on content. +- +- Arguments: +- sequence: the sequence to check, either a string or Bio.Seq +- +- Returns: +- True if more than 80% of characters are nucleotide bases +- """ +- other = str(sequence).lower() +- for char in "acgtn": +- other = other.replace(char, "") +- return len(other) < 0.2 * len(sequence) +- +- + def records_contain_shotgun_scaffolds(records: List[Record]) -> bool: + """ Check if given records contain a WGS master record or supercontig record + +diff --git a/antismash/common/secmet/features/region.py b/antismash/common/secmet/features/region.py +index 79f8f9a2..f0af7a52 100644 +--- a/antismash/common/secmet/features/region.py ++++ b/antismash/common/secmet/features/region.py +@@ -162,6 +162,9 @@ def write_to_genbank(self, filename: str = None, directory: str = None, record: + cluster_record.annotations["taxonomy"] = record.annotations.get("taxonomy", []) + cluster_record.annotations["data_file_division"] = record.annotations.get("data_file_division", 'UNK') + cluster_record.annotations["comment"] = record.annotations.get("comment", '') ++ # biopython does not persist the molecule_type annotation in slices, ++ # despite it being required for output to the genbank format ++ cluster_record.annotations["molecule_type"] = record.annotations["molecule_type"] + + # update the antiSMASH annotation to include some cluster details + comment_end_marker = "##antiSMASH-Data-END" +diff --git a/antismash/common/secmet/features/test/test_region.py b/antismash/common/secmet/features/test/test_region.py +index 0d34046a..364fc2a5 100644 +--- a/antismash/common/secmet/features/test/test_region.py ++++ b/antismash/common/secmet/features/test/test_region.py +@@ -7,7 +7,6 @@ + from tempfile import NamedTemporaryFile + import unittest + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from helperlibs.bio import seqio + +@@ -138,7 +137,7 @@ def test_probabilities(self): + assert Region(candidate_clusters=candidates, subregions=subs).probabilities == [0.1, 0.7] + + def test_genbank(self): +- dummy_record = Record(Seq("A"*100, generic_dna)) ++ dummy_record = Record(Seq("A"*100)) + clusters = [create_protocluster(3, 20, "prodA"), + create_protocluster(25, 41, "prodB")] + for cluster in clusters: +@@ -164,7 +163,7 @@ def test_genbank(self): + assert new.probabilities == region.probabilities + + def test_prepeptide_adjustment(self): +- dummy_record = Record(Seq("A"*400, generic_dna)) ++ dummy_record = Record(Seq("A"*400)) + subregion = DummySubRegion(start=100, end=300) + dummy_record.add_subregion(subregion) + region = Region(subregions=[subregion]) +diff --git a/antismash/common/secmet/record.py b/antismash/common/secmet/record.py +index 95e63725..a177b789 100644 +--- a/antismash/common/secmet/record.py ++++ b/antismash/common/secmet/record.py +@@ -16,7 +16,7 @@ + import logging + from typing import Any, Dict, List, Optional, Sequence, Type, Tuple, Union, cast + +-from Bio import Alphabet, SeqIO ++from Bio import SeqIO + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation + from Bio.SeqRecord import SeqRecord +@@ -467,6 +467,8 @@ def to_biopython(self) -> SeqRecord: + bio_features: List[SeqFeature] = [] + for feature in sorted(features): + bio_features.extend(feature.to_biopython()) ++ if "molecule_type" not in self._record.annotations: ++ self._record.annotations["molecule_type"] = "DNA" + return SeqRecord(self.seq, id=self._record.id, name=self._record.name, + description=self._record.description, + dbxrefs=self.dbxrefs, features=bio_features, +@@ -653,9 +655,10 @@ def from_biopython(seq_record: SeqRecord, taxon: str) -> "Record": + postponed_features[kind.FEATURE_TYPE] = (kind, []) + + assert isinstance(seq_record, SeqRecord), type(seq_record) +- if seq_record.seq and isinstance(seq_record.seq, Seq): +- if isinstance(seq_record.seq.alphabet, Alphabet.ProteinAlphabet): +- raise SecmetInvalidInputError("protein records are not supported") ++ if seq_record.annotations.get("molecule_type", "DNA") != "DNA": ++ raise SecmetInvalidInputError("protein records are not supported") ++ if seq_record.seq and not Record.is_nucleotide_sequence(seq_record.seq): ++ raise SecmetInvalidInputError("protein records are not supported") + transl_table = 1 # standard + if str(taxon) == "bacteria": + transl_table = 11 # bacterial, archea, plant plastid code +@@ -831,11 +834,11 @@ def get_aa_translation_from_location(self, location: FeatureLocation, + string_version = str(seq) + for invalid in "*BJOUZ": + string_version = string_version.replace(invalid, "X") +- seq = Seq(string_version, Alphabet.generic_protein) + + if "-" in str(seq): +- seq = Seq(str(seq).replace("-", ""), Alphabet.generic_protein) +- return seq ++ seq = Seq(str(seq).replace("-", "")) ++ ++ return Seq(string_version) + + def get_cds_features_within_regions(self) -> List[CDSFeature]: # pylint: disable=invalid-name + """ Returns all CDS features in the record that are located within a +@@ -958,3 +961,18 @@ def strip_antismash_annotations(self) -> None: + # clean up antiSMASH annotations in CDS features + for feature in self.get_cds_features(): + feature.strip_antismash_annotations() ++ ++ @staticmethod ++ def is_nucleotide_sequence(sequence: Union[Seq, str]) -> bool: ++ """ Determines if a sequence is a nucleotide sequence based on content. ++ ++ Arguments: ++ sequence: the sequence to check, either a string or Bio.Seq ++ ++ Returns: ++ True if more than 80% of characters are nucleotide bases ++ """ ++ other = str(sequence).lower() ++ for char in "acgtn": ++ other = other.replace(char, "") ++ return len(other) < 0.2 * len(sequence) +diff --git a/antismash/common/secmet/test/test_circular_conversion.py b/antismash/common/secmet/test/test_circular_conversion.py +index e001480b..1619d425 100644 +--- a/antismash/common/secmet/test/test_circular_conversion.py ++++ b/antismash/common/secmet/test/test_circular_conversion.py +@@ -6,7 +6,7 @@ + + import unittest + +-from Bio.Seq import UnknownSeq ++from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature + from Bio.SeqRecord import SeqRecord + +@@ -16,7 +16,7 @@ + + class TestBridgeConversion(unittest.TestCase): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 15, strand=1), + FeatureLocation(18, 21, strand=1), + FeatureLocation(0, 3, strand=1), +@@ -25,6 +25,7 @@ def setUp(self): + self.seqcds = SeqFeature(loc, type="CDS") + self.seqgene = SeqFeature(loc, type="gene") + self.seqrec.annotations["topology"] = "circular" ++ self.seqrec.annotations["molecule_type"] = "DNA" + + def test_bridge_in_linear_record(self): + self.seqrec.annotations["topology"] = "linear" +@@ -110,7 +111,7 @@ def test_gene_with_no_id(self): + + class TestSingleLower(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 15, strand=1), + FeatureLocation(18, 21, strand=1), + FeatureLocation(0, 9, strand=1)], +@@ -122,7 +123,7 @@ def setUp(self): + + class TestSingleUpper(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 21, strand=1), + FeatureLocation(0, 3, strand=1), + FeatureLocation(6, 9, strand=1)], +@@ -133,7 +134,7 @@ def setUp(self): + + class TestSingleBoth(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 21, strand=1), + FeatureLocation(0, 9, strand=1)], + operator="join") +diff --git a/antismash/common/secmet/test/test_secmet.py b/antismash/common/secmet/test/test_secmet.py +index d802d6fd..65ac7b2c 100644 +--- a/antismash/common/secmet/test/test_secmet.py ++++ b/antismash/common/secmet/test/test_secmet.py +@@ -8,7 +8,6 @@ + import unittest + + import Bio.SeqIO +-from Bio.Alphabet.IUPAC import IUPACProtein + from Bio.Seq import Seq + from Bio.SeqFeature import FeatureLocation, SeqFeature + +@@ -78,7 +77,7 @@ def test_protein_sequences_caught(self): + assert isinstance(before.seq, Seq) + Record.from_biopython(before, taxon="bacteria") + +- before.seq = Seq("AAAA", IUPACProtein()) ++ before.annotations["molecule_type"] = "protein" + with self.assertRaisesRegex(ValueError, "protein records are not supported"): + Record.from_biopython(before, taxon="bacteria") + +@@ -789,3 +788,20 @@ def test_nonoverlapping_location(self): + cds = CDSFeature(FeatureLocation(12, 18, 1), locus_tag="test", protein_id="prot", translation="MA") + with self.assertRaisesRegex(ValueError, "same name for mapping"): + record.add_cds_feature(cds) ++ ++ ++class TestIsNuclSeq(unittest.TestCase): ++ def test_seq(self): ++ # > 20% ++ for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: ++ assert Record.is_nucleotide_sequence(Seq(seq)) ++ # edge case == 20% should be failure ++ assert not Record.is_nucleotide_sequence(Seq("AGFTC")) ++ # and less than 20% ++ assert not Record.is_nucleotide_sequence(Seq("AGFTCF")) ++ ++ def test_str(self): ++ for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: ++ assert Record.is_nucleotide_sequence(seq) ++ assert not Record.is_nucleotide_sequence("AGFTC") ++ assert not Record.is_nucleotide_sequence("AGFTCF") +diff --git a/antismash/common/serialiser.py b/antismash/common/serialiser.py +index a9ca198d..9436b60b 100644 +--- a/antismash/common/serialiser.py ++++ b/antismash/common/serialiser.py +@@ -10,8 +10,6 @@ + import logging + from typing import Any, Dict, IO, List, Union + +-import Bio.Alphabet +-import Bio.Alphabet.IUPAC + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, Reference + from Bio.SeqRecord import SeqRecord +@@ -179,8 +177,10 @@ def rebuild_references(annotations: Dict) -> Dict[str, List[Reference]]: + + def sequence_to_json(sequence: Seq) -> Dict[str, str]: + """ Constructs a JSON object that represents a Seq sequence """ +- return {"data": str(sequence), +- "alphabet": str(sequence.alphabet).rsplit('()')[0]} # DNA() -> DNA ++ return { ++ "data": str(sequence), ++ "alphabet": "DNA", # for compatibility, removable on schema version change ++ } + + + def sequence_from_json(data: Union[str, Dict]) -> Seq: +@@ -188,12 +188,7 @@ def sequence_from_json(data: Union[str, Dict]) -> Seq: + if isinstance(data, str): + data = json.loads(data) + assert isinstance(data, dict) +- alphabet = data["alphabet"] +- if "IUPAC" in alphabet: +- alphabet_class = getattr(Bio.Alphabet.IUPAC, alphabet) +- else: +- alphabet_class = getattr(Bio.Alphabet, alphabet) +- return Seq(data["data"], alphabet=alphabet_class()) ++ return Seq(data["data"]) + + + def feature_to_json(feature: SeqFeature) -> Dict[str, Any]: +diff --git a/antismash/common/test/helpers.py b/antismash/common/test/helpers.py +index 315c8fcc..66ff2a63 100644 +--- a/antismash/common/test/helpers.py ++++ b/antismash/common/test/helpers.py +@@ -13,7 +13,6 @@ + + import os + +-from Bio.Seq import Seq + from helperlibs.wrappers.io import TemporaryDirectory + + import antismash +@@ -46,8 +45,9 @@ def get_simple_options(module, args): + + class DummyRecord(Record): + "class for generating a Record like data structure" +- def __init__(self, features=None, seq='FAKESEQ', taxon='bacteria'): ++ def __init__(self, features=None, seq='AGCTACGT', taxon='bacteria'): + super().__init__(seq, transl_table=11 if taxon == 'bacteria' else 1) ++# self.annotations["molecule_type"] = "DNA" + if features: + for feature in features: + self.add_feature(feature) +diff --git a/antismash/common/test/test_record_processing.py b/antismash/common/test/test_record_processing.py +index 3deac06c..3f4c9852 100644 +--- a/antismash/common/test/test_record_processing.py ++++ b/antismash/common/test/test_record_processing.py +@@ -154,23 +154,6 @@ def test_no_change(self): + assert new.seq == self.record.seq + + +-class TestIsNuclSeq(unittest.TestCase): +- def test_seq(self): +- # > 20% +- for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: +- assert record_processing.is_nucl_seq(Seq(seq)) +- # edge case == 20% should be failure +- assert not record_processing.is_nucl_seq(Seq("AGFTC")) +- # and less than 20% +- assert not record_processing.is_nucl_seq(Seq("AGFTCF")) +- +- def test_str(self): +- for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: +- assert record_processing.is_nucl_seq(seq) +- assert not record_processing.is_nucl_seq("AGFTC") +- assert not record_processing.is_nucl_seq("AGFTCF") +- +- + class TestPreprocessRecords(unittest.TestCase): + def setUp(self): + class DummyModule: +diff --git a/antismash/modules/pfam2go/test/test_pfam2go.py b/antismash/modules/pfam2go/test/test_pfam2go.py +index 8f772dd6..03b80839 100644 +--- a/antismash/modules/pfam2go/test/test_pfam2go.py ++++ b/antismash/modules/pfam2go/test/test_pfam2go.py +@@ -8,7 +8,6 @@ + + from typing import Dict + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from Bio.SeqFeature import FeatureLocation + +@@ -97,7 +96,7 @@ def test_get_gos(self): + + def test_blank_records(self): + blank_no_pfams = DummyRecord() +- blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna)) ++ blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT")) + fake_pfam = DummyPFAMDomain(identifier="PF00000") + blank_no_ids.add_pfam_domain(fake_pfam) + +diff --git a/antismash/modules/tta/test/test_tta.py b/antismash/modules/tta/test/test_tta.py +index e03f9fc5..eb27d548 100644 +--- a/antismash/modules/tta/test/test_tta.py ++++ b/antismash/modules/tta/test/test_tta.py +@@ -7,7 +7,6 @@ + from argparse import Namespace + import unittest + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, FeatureLocation + +@@ -19,7 +18,7 @@ + class TtaTest(unittest.TestCase): + def setUp(self): + # locations: VVV VVV +- record = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna)) ++ record = Record(Seq("ATGTTATGAGGGTCATAACAT")) + + record.add_cds_feature(DummyCDS(0, 9, strand=1)) + record.add_cds_feature(DummyCDS(12, 21, strand=-1)) +diff --git a/setup.py b/setup.py +index cba1f338..b0b02341 100644 +--- a/setup.py ++++ b/setup.py +@@ -16,7 +16,7 @@ def read(fname): + + install_requires = [ + 'numpy', +- 'biopython >=1.71,<1.77', ++ 'biopython >=1.78', + 'helperlibs', + 'jinja2', + 'joblib', + +From 98dbffe5a726444bdf9b24c8f8664533a3d450eb Mon Sep 17 00:00:00 2001 +From: Simon Shaw +Date: Tue, 27 Oct 2020 10:01:59 +0100 +Subject: [PATCH 2/2] chore: bump minimum python version to 3.7 + +--- + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index b0b02341..c7709966 100644 +--- a/setup.py ++++ b/setup.py +@@ -95,7 +95,7 @@ def run_tests(self): + + setup( + name="antismash", +- python_requires='>=3.5', ++ python_requires='>=3.7', + version=read_version(), + packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]), + package_data={ diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 00000000000..947e4cda9a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..496d7c1314c --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 00000000000..75cf15432a6 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] + +# use correct compiler flags + +# don't use -static when linking, since that implies requiring glibc-static to be installed +buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' From beac104fbfb6a6d2c785c30aa0ae3465909705c5 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 21 May 2021 14:52:44 +0950 Subject: [PATCH 035/528] adding easyconfigs: MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb --- ...MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..5f5569489c8 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,52 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# Software License:: MIT +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'MetaPhlAn' +version = '3.0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/MetaPhlAn' +description = """MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data """ + +source_urls = ['https://github.com/biobakery/MetaPhlAn/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['de965469e4f93e3dd5c9e2dac8914f7debd242c196f343cd7cefd8c7faddd33c'] + +toolchain = {'name':'foss', 'version':'2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Perl', '5.30.2'), + ('Bowtie2', '2.4.1'), + ('SAMtools', '1.10'), + ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('MAFFT', '7.470', '-with-extensions'), + ('RAxML', '8.2.12', '-hybrid-avx2'), + ('DIAMOND', '2.0.4'), + ('trimAl', '1.4.1'), + ('FastTree', '2.1.11'), +] + +modextrapaths = { + 'PATH': 'bin', +} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], + 'dirs': ['bin', 'lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': 'metaphlan'} + +moduleclass = 'bio' From 8afa13565408a3a9683c848d36b984b5a9121c51 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 21 May 2021 16:00:36 +0950 Subject: [PATCH 036/528] Syntax fix --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 5f5569489c8..7824b57fa65 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -15,13 +15,14 @@ version = '3.0.9' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/biobakery/MetaPhlAn' -description = """MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data """ +description = """MetaPhlAn is a computational tool for profiling the composition + of microbial communities from metagenomic shotgun sequencing data """ source_urls = ['https://github.com/biobakery/MetaPhlAn/archive'] sources = ['%(version)s.tar.gz'] checksums = ['de965469e4f93e3dd5c9e2dac8914f7debd242c196f343cd7cefd8c7faddd33c'] -toolchain = {'name':'foss', 'version':'2020a'} +toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), From 160966ddf4bc2b075025febaf75531bd84798d3c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 22 May 2021 18:41:38 +0950 Subject: [PATCH 037/528] lib PATH + --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 7824b57fa65..6bba4f19e22 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -39,7 +39,8 @@ dependencies = [ ] modextrapaths = { - 'PATH': 'bin', + 'LIBRARY_PATH': 'lib', + 'LD_LIBRARY_PATH': 'lib' } sanity_check_paths = { From 0f762c1d8482bb7f0f5b8fb3639a1ba7222d16c6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 28 May 2021 11:44:58 +0950 Subject: [PATCH 038/528] MAFFT ver downgrade to 7.453 --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 6bba4f19e22..d42e309a208 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.470', '-with-extensions'), + ('MAFFT', '7.453 53 53 53 53 ', '-with-extensions'), ('RAxML', '8.2.12', '-hybrid-avx2'), ('DIAMOND', '2.0.4'), ('trimAl', '1.4.1'), From 5dbf3125e17486b0b568ff87949f7f1b9a9bdc85 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 28 May 2021 12:01:07 +0950 Subject: [PATCH 039/528] MAFFT ver typo fix --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d42e309a208..c617510fa38 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.453 53 53 53 53 ', '-with-extensions'), + ('MAFFT', '7.453', '-with-extensions'), ('RAxML', '8.2.12', '-hybrid-avx2'), ('DIAMOND', '2.0.4'), ('trimAl', '1.4.1'), From 1dfc81719e8294fd93a131fa89485599ff6a73fb Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 3 Jun 2021 16:41:41 +0950 Subject: [PATCH 040/528] pip + dep settings turned on --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index c617510fa38..d49afd6c48a 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -38,6 +38,10 @@ dependencies = [ ('FastTree', '2.1.11'), ] +use_pip = True +sanity_pip_check = True +download_dep_fail = True + modextrapaths = { 'LIBRARY_PATH': 'lib', 'LD_LIBRARY_PATH': 'lib' From fa8753ca8e1fcf07d0594c4feb09054491134d0e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 5 Jun 2021 08:27:50 +0200 Subject: [PATCH 041/528] adding easyconfigs: Extrae-3.8.3-gompi-2021a.eb, libdwarf-20210305-GCCcore-10.3.0.eb, libelf-0.8.13-GCCcore-10.3.0.eb --- .../e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 33 ++++++++++++++++++ .../libdwarf-20210305-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ .../l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb | 29 ++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb new file mode 100644 index 00000000000..a58b66ffa82 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +name = 'Extrae' +version = '3.8.3' + +homepage = 'https://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by +the Performance Tools group at BSC. Extrae is capable of instrumenting +applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 +using different instrumentation approaches. The information gathered by +Extrae typically includes timestamped events of runtime calls, +performance counters and source code references. Besides, Extrae +provides its own API to allow the user to manually instrument his or her +application.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('libunwind', '1.5.0'), + ('libxml2', '2.9.10'), + ('libdwarf', '20210305'), + ('PAPI', '6.0.0.1'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4d501a86e34 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '20210305' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.prevanders.net'] +sources = [SOURCE_TAR_GZ] +checksums = ['b86bef41725326d13ee3e7e45b929e0ca97b639e93cc1a9214c90a1774fa1c1a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] +dependencies = [ + ('libelf', '0.8.13'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..155b9c5bd4e --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'https://sourceware.org/elfutils' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://fossies.org/linux/misc/old/'] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' From f0862d77807f79aaa8e35fedde5608e13eb7b8c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 14:39:32 +0200 Subject: [PATCH 042/528] add commented out post-install commands to download antiSMASH databases --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index 57fe702e6cf..a0c8a90bc51 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -46,8 +46,6 @@ components = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('helperlibs', '0.2.1', { 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], @@ -72,12 +70,25 @@ exts_list = [ 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch ], + # use http mirrors for ftp URLs + 'preinstallopts': "sed -i 's/ftp:/http:/g' antismash/download_databases.py && ", + # run additional commands to download databases and check prerequisites, + # which creates some missing .pkl files (which requires the databases); + # this is not done by default because the resulting installation is pretty big (~18GB) + # 'postinstallcmds': [ + # "download-antismash-databases", + # # check prerequisites, which also creates some missing .pkl files in the installation... + # "antismash --check-prereqs", + # ], }), ] sanity_check_paths = { 'files': ['bin/antismash', 'bin/meme'], - 'dirs': [], + 'dirs': [ + # antismash/databases subdirectory is only populated when postinstallcmds above are commented out + # 'lib/python%(pyshortver)s/site-packages/antismash/databases', + ], } sanity_check_commands = [ From 2f5807fe2fa618ae328a4bb05a022bce902f4fac Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sun, 13 Jun 2021 00:39:46 +0950 Subject: [PATCH 043/528] dep issue fix with pip --- ...MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 19 ++----------------- 1 file changed, 2 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d49afd6c48a..f484f3c9d9b 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -27,25 +27,12 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), - ('Perl', '5.30.2'), - ('Bowtie2', '2.4.1'), - ('SAMtools', '1.10'), - ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.453', '-with-extensions'), - ('RAxML', '8.2.12', '-hybrid-avx2'), - ('DIAMOND', '2.0.4'), - ('trimAl', '1.4.1'), - ('FastTree', '2.1.11'), ] use_pip = True +use_pip_for_deps = True sanity_pip_check = True -download_dep_fail = True - -modextrapaths = { - 'LIBRARY_PATH': 'lib', - 'LD_LIBRARY_PATH': 'lib' -} +download_dep_fail = False sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], @@ -53,6 +40,4 @@ sanity_check_paths = { } sanity_check_commands = [('%(namelower)s', '-h')] -options = {'modulename': 'metaphlan'} - moduleclass = 'bio' From d28d6954e77fd481405cdad2dbf1fb792d4d2a30 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 00:38:29 +0950 Subject: [PATCH 044/528] adding easyconfigs: RAPSearch2-2.24-GCC-9.3.0.eb --- .../r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb new file mode 100644 index 00000000000..80948486498 --- /dev/null +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU GPLv1 +# +# Notes:: +## + +easyblock = 'CmdCp' + +name = 'RAPSearch2' +version = '2.24' + +homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' +description = """ +RAPSearch stands for Reduced Alphabet based Protein similarity Search +""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] +sources = ['%(name)s.24_64bits.tar.gz'] +checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] + +install_cmd = './install' + +skipsteps = ['configure', 'build'] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], + 'dirs': [], +} + +moduleclass = 'bio' From 70c84c0d3d4dd58a2c47853ff5453c152387ebdd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 22 Jun 2021 18:38:33 +0100 Subject: [PATCH 045/528] adding easyconfigs: PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb, imageio-2.9.0-fosscuda-2020b.eb --- .../i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 26 ++++++++++ ...ch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb | 51 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..a67dbeea4c2 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..380a99eee47 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,51 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PyTorch3D' +version = '0.4.0' +local_pytorch_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = "https://pytorch3d.org/" +description = """PyTorch3D is FAIR's library of reusable components for deep learning with 3D data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('tqdm', '4.60.0'), + ('PyTorch', local_pytorch_version), + ('imageio', '2.9.0'), + ('IPython', '7.18.1'), + ('torchvision', '0.9.1', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('portalocker', '2.3.0', { + 'checksums': ['4e913d807aa6598c320e8a50c50e2ee0602bc45240b485e3f8bc06f13060084c'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yacs', '0.1.8', { + 'checksums': ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'], + }), + ('iopath', '0.1.8', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e11029c30ee77616b3efd82888aa80941d12afcc5940c2ef57e04a8e93a10f9f'], + }), + ('fvcore', '0.1.5.post20210617', { + 'checksums': ['1f1fb91b82166f85ed0f7da8906e87688de9e1b4879b478dc3969d93d24f0379'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/facebookresearch/%(namelower)s/archive'], + 'checksums': ['6f33c45c8b698b068ff267287ad490dc2f8f48ad2f486175438b0426575e391a'], + }), +] + +moduleclass = 'tools' From 6002d30c4613f4f0262ccc909e761a38cd6bb54e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 23 Jun 2021 13:01:18 +0100 Subject: [PATCH 046/528] use the correct tqdm version --- .../p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb index 380a99eee47..9be26b1a985 100644 --- a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('PyTorch', local_pytorch_version), ('imageio', '2.9.0'), ('IPython', '7.18.1'), From 27165fa55ad4474fd28f977ec20c73538ba17b90 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 25 Jun 2021 17:35:55 +0950 Subject: [PATCH 047/528] easyblock change --- .../r/RAPSearch2/RAPSearch2-2.24.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb new file mode 100644 index 00000000000..679405c3428 --- /dev/null +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU GPLv1 +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'RAPSearch2' +version = '2.24' + +homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' +description = """ +RAPSearch stands for Reduced Alphabet based Protein similarity Search +""" + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] +sources = ['%(name)s.24_64bits.tar.gz'] +checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] + +skipsteps = ['configure'] +build_cmd = './install' +parallel = 1 + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], + 'dirs': [], +} + +moduleclass = 'bio' From 0e144592d4bef142a5866344b79399d2378ae2bf Mon Sep 17 00:00:00 2001 From: manifest Date: Fri, 25 Jun 2021 17:17:06 +0930 Subject: [PATCH 048/528] Delete RAPSearch2-2.24-GCC-9.3.0.eb Change to lagacy toolchange for compilation. --- .../r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb deleted file mode 100644 index 80948486498..00000000000 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GNU GPLv1 -# -# Notes:: -## - -easyblock = 'CmdCp' - -name = 'RAPSearch2' -version = '2.24' - -homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' -description = """ -RAPSearch stands for Reduced Alphabet based Protein similarity Search -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] -sources = ['%(name)s.24_64bits.tar.gz'] -checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] - -install_cmd = './install' - -skipsteps = ['configure', 'build'] - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], - 'dirs': [], -} - -moduleclass = 'bio' From 767a96e503f0a9497382552865649661af9cfa59 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 17:02:52 +0200 Subject: [PATCH 049/528] adding easyconfigs: itac-2021.2.0.eb --- easybuild/easyconfigs/i/itac/itac-2021.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.2.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb new file mode 100644 index 00000000000..b95225dd483 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +name = 'itac' +version = '2021.2.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] +checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +# license file +# license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' From b4d94f8f4c2196a3a5d2c2160f3fc43a4d417b2f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 30 Jun 2021 14:51:33 +0200 Subject: [PATCH 050/528] adding easyconfigs: CUDAcore-11.4.0.eb, CUDA-11.4.0-GCC-10.3.0.eb --- .../c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb | 20 ++++++++++++ .../easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb | 31 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..4f3b65f368c --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb @@ -0,0 +1,20 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' +name = 'CUDA' +version = '11.4.0' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +dependencies = [('CUDAcore', version, '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb new file mode 100644 index 00000000000..e5e87706325 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'EB_CUDA' + +name = 'CUDAcore' +version = '11.4.0' +local_nv_version = '470.42.01' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'd219db30f7415a115a4ea22bdbb5984b0a18f7f891cad6074c5da45d223aaa4b', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '6eb2fd0d9d5bc39fb243b5e1789ff827f325d098cd1fbb828a0499552b9544cc', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'f0c8e80d98a601ddca031b6764459984366008c7d3847e7c7f99b36bd4438e3c' + } +] + +moduleclass = 'system' From 1c4b21aed1fe158f2dd7cf2848c6f453ce009576 Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 1 Jul 2021 09:41:28 +0930 Subject: [PATCH 051/528] Update easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb index 679405c3428..38c5a263b4c 100644 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb @@ -18,7 +18,7 @@ description = """ RAPSearch stands for Reduced Alphabet based Protein similarity Search """ -toolchain = {'name': 'system', 'version': 'system'} +toolchain = SYSTEM source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] sources = ['%(name)s.24_64bits.tar.gz'] From 501b7e18fb613b38848eb6afde890c0b7e52f587 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 6 Jul 2021 10:03:21 +0200 Subject: [PATCH 052/528] CUDA 11.4.0 is removed --- .../c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb deleted file mode 100644 index 4f3b65f368c..00000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'Bundle' -name = 'CUDA' -version = '11.4.0' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -dependencies = [('CUDAcore', version, '', True)] - -altroot = 'CUDAcore' - -moduleclass = 'system' From ff3497d119ba937e9425b98996add8713d7f7367 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 28 Aug 2021 15:04:32 +0100 Subject: [PATCH 053/528] remove unneeded source_urls --- easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb index a67dbeea4c2..6297f03ff60 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -9,7 +9,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] From 9eed9be9b112b27b7df683412662f46a403b62fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 16 Sep 2021 19:40:11 +0200 Subject: [PATCH 054/528] adding easyconfigs: Qt5-5.15.2-GCCcore-11.2.0.eb --- .../q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0ae4b2b7fe1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -0,0 +1,69 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', +] +checksums = [ + '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch + '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch + '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + # deps for QtWebEngine + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.6', '-bare'), + ('re2c', '2.2'), +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('GLib', '2.69.1'), + ('PCRE2', '10.37'), + ('libpng', '1.6.37'), + # deps for QtWebEngine + ('X11', '20210802'), + ('fontconfig', '2.13.94'), + ('DBus', '1.13.18'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.2'), + ('libjpeg-turbo', '2.0.6'), + ('NSS', '3.69'), + ('snappy', '1.1.9'), + ('JasPer', '2.0.33'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', True), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' From 3c1037760e5d7b17f6e49d29b4eadd140b99f814 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 16:21:41 +0200 Subject: [PATCH 055/528] adding easyconfigs: IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- ...-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb new file mode 100644 index 00000000000..1a94253258b --- /dev/null +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -0,0 +1,65 @@ +# Thomas Hofffmann, EMBL Heidelberg, structures-it@embl.de, 2021/09 +easyblock = 'Tarball' # there is no setup.py -> unpack tarball and move to site-packages in postinstall. + +name = 'IsoNet' +# There is no version tag available in github. Using commit and date instead. +local_commit = '674f67f1afb8aa1353c0d67ccb55263c1f20576f' +local_version = '0.1' +local_commit_date = '20210822' +local_commit_count = '04' +version = '%s_%s_%s_%s' % (local_version, local_commit_date, local_commit_count, local_commit[:7]) + +homepage = 'https://github.com/Heng-Z/IsoNet' +description = """IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains +deep convolutional neural networks to reconstruct meaningful contents in the mis +sing wedge for electron tomography, and to increase signal-to-noise ratio, +using the information learned from the original tomogram. The software requires +tomograms as input. Observing at about 30A resolution, the IsoNet generated +tomograms are largely isotropic.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/Heng-Z/IsoNet/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['dac1583bbab0d6b09496657b5d237b9c35c9a70ee9c0089a174e571b78892d49'] + +install_type = 'subdir' +postinstallcmds = [ + 'find %(installdir)s/isonet -name \'*.pyc\' -exec rm {} \\;' + '&& mv %(installdir)s/isonet %(installdir)s/lib/python%(pyshortver)s/site-packages/IsoNet' +] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), + ('PyQt5', '5.15.1'), + ('SciPy-bundle', '2020.11'), + ('mrcfile', '1.3.0'), + ('tqdm', '4.60.0'), + ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! +] +sanity_pip_check = True +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('fire', '0.4.0', { + 'modulename': 'fire', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'use_pip': True, + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), +] + +modextrapaths = { + 'PATH': 'lib/python%(pyshortver)s/site-packages/IsoNet/bin', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/' +} +sanity_check_commands = [ + 'isonet.py check', + 'isonet.py --help', +] +sanity_check_paths = { + 'files': [], + 'dirs': ["lib/python%(pyshortver)s/site-packages/IsoNet"] +} + +moduleclass = 'bio' From 921bc1f6781802a307117534796fd67d666ada83 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 28 Sep 2021 16:35:39 +0200 Subject: [PATCH 056/528] Update IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 1a94253258b..6efea4b1dbe 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,7 +38,6 @@ dependencies = [ ('tqdm', '4.60.0'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] -sanity_pip_check = True exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { From 84f1d6f60403d38f2e27c7ed27f09749f4e05f71 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:17:28 +0200 Subject: [PATCH 057/528] downgrade tqdm dep --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 6efea4b1dbe..05c2b7e4727 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('PyQt5', '5.15.1'), ('SciPy-bundle', '2020.11'), ('mrcfile', '1.3.0'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] exts_defaultclass = 'PythonPackage' From 6fc65348415f87112ae451f1a6429f756f2d83c0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:42:55 +0200 Subject: [PATCH 058/528] exts_default_options --- .../IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 05c2b7e4727..48e8d55811f 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,12 +38,15 @@ dependencies = [ ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { 'modulename': 'fire', 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'use_pip': True, 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), ] From 35343d3ca7870297867f7f2e72abebaead56611a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 18 Oct 2021 15:45:51 +0000 Subject: [PATCH 059/528] Version bump. Improvements on JAX etc --- ...-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 00000000000..66d8b4e92b2 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('TensorFlow', local_tf_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 1f3f8256355b50c2fbe70bcf36289502835beed9 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 18 Oct 2021 15:48:26 +0000 Subject: [PATCH 060/528] cleanup --- .../Code_Saturne-6.1.1-gpsmkl-2019a.1.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb diff --git a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb deleted file mode 100644 index 53c5c098a0b..00000000000 --- a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb +++ /dev/null @@ -1,56 +0,0 @@ -# easyconfig file for Code_Saturne -# author: Metin Cakircali (Juelich Supercomputing Centre) -name = 'Code_Saturne' -version = '6.1.1' - -# extra option for the SLURM batch system -slurm = True - -homepage = 'https://www.code-saturne.org' -description = """Code_Saturne solves the Navier-Stokes equations -for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, -laminar or turbulent, incompressible or weakly dilatable, -isothermal or not, with scalars transport if required. - -Code_Saturne %(version)s%(versionsuffix)s is installed in -$EBROOTCODE_SATURNE -""" -site_contacts = 'a.strube@fz-juelich.de' - -toolchain = {'name': 'gpsmkl', 'version': '2019a.1'} -toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} - -sources = [{ - 'source_urls': ['https://github.com/code-saturne/code_saturne/archive/'], - 'filename': 'v%(version)s.tar.gz' -}] - -builddependencies = [ - ('Autotools', '20180311'), - ('gettext', '0.19.8.1'), - ('Bison', '3.3.2'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('Python', '3.6.8'), - ('PyQt5', '5.11.3', '-Python-%(pyver)s'), - ('HDF5', '1.10.5'), - ('MED', '4.0.0'), - ('CGNS', '4.1.1'), - ('ParMETIS', '4.0.3'), - ('SCOTCH', '6.0.6'), - ('ParaView', '5.6.0', '-Python-%(pyver)s', ('gpsmkl', '2019a.1')), -] - -# better to configure these dependents explicitly -configopts = ['--with-med=$EBROOTMED --with-cgns=$EBROOTCGNS \ - --with-metis=$EBROOTPARMETIS --with-scotch=$EBROOTSCOTCH'] - -parallel = 48 - -modloadmsg = "To benefit from shell completion for %(name)s commands and\n" -modloadmsg += "options, you may also source a bash completion file by;\n" -modloadmsg += ". $CS_BASH\n" - -moduleclass = 'cae' From ce5cfe3cc8441bdb206009b1acc83e73ee78a840 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 20:36:12 +0200 Subject: [PATCH 061/528] adding easyconfigs: mold-0.9.6-GCCcore-11.2.0.eb, xxHash-0.8.0-GCCcore-11.2.0.eb --- .../m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb | 31 +++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1b0b1af41f3 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '0.9.6' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['348e1b893d3520322b1e047b5abf040e56ad92de5643e67652ede87b9d694f60'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('xxHash', '0.8.0'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..db5bf12cc24 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.0' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7054c3ebd169c97b64a92d7b994ab63c70dd53a06974f1f630ab782c28db0f4f'] + +builddependencies = [ + ('binutils', '2.37'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' From 4648705eaa0cccd6dba5feb1db960c1f6a722109 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 15:39:55 +1050 Subject: [PATCH 062/528] adding easyconfigs: cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb --- ..._Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..237512b3ae7 --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,44 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '24.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = "cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9aa75ef3d00e9983772021dca3c5595df5ea23c39fb0004e4330e55edc782002'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('bx-python', '0.8.9', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'cupcake'} + +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 6530e4a954893149fe28c2a773f89740e1660a72 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 15:47:12 +1050 Subject: [PATCH 063/528] requires PR #14277, #14276, #14245 --- .../Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ec5278eb0ad --- /dev/null +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'Cogent' +version = '8.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/Cogent' +description = """ +Cogent is a tool for reconstructing the coding genome using high-quality +full-length transcriptome sequences. It is designed to be used on Iso-Seq data +and in cases where there is no reference genome or the ref genome is highly +incomplete. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('scikit-image', '0.17.1', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('bx-python', '0.8.9', versionsuffix), + ('parasail', '2.4.2'), + ('CapnProto', '0.8.0'), + ('minimap2', '2.17'), + ('Mash', '2.2'), + ('cDNA_Cupcake', '24.2.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/run_mash.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'Cogent'} + +moduleclass = 'bio' From 271ea11ee7062dcaf89ee651b2095fa417103cd7 Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 16:21:12 +1030 Subject: [PATCH 064/528] pip check + --- .../cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 237512b3ae7..47cd3dce2d2 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -30,6 +30,7 @@ use_pip = True options = {'modulename': 'cupcake'} +sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step From a5e9428d0727e0cd524e371ae7db14761051318c Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 16:34:47 +1030 Subject: [PATCH 065/528] pip dep PuLP + --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index ec5278eb0ad..d54847566f1 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -38,6 +38,10 @@ dependencies = [ ('cDNA_Cupcake', '24.2.0', versionsuffix), ] +download_dep_fail = True +use_pip = True + +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/run_mash.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 5f07741edd8a5c107aa15b3816bd8dba152afc4e Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 21:16:46 +1030 Subject: [PATCH 066/528] deps [parasail --> python-parasail] --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index d54847566f1..3c93ab37e8c 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('parasail', '2.4.2'), + ('python-parasail', '1.2.3', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 3d4bb965ebb2ac73647cc2dc98a63b9ff42718a9 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 5 Nov 2021 19:43:23 +1050 Subject: [PATCH 067/528] comply with c++11 standard -- ABI bug --- .../{RAPSearch2-2.24.eb => RAPSearch2-2.24-GCC-9.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/RAPSearch2/{RAPSearch2-2.24.eb => RAPSearch2-2.24-GCC-9.3.0.eb} (82%) diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb similarity index 82% rename from easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb rename to easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb index 38c5a263b4c..f1694491013 100644 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb @@ -18,10 +18,11 @@ description = """ RAPSearch stands for Reduced Alphabet based Protein similarity Search """ -toolchain = SYSTEM +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-D_GLIBCXX_USE_CXX11_ABI=0'} source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] -sources = ['%(name)s.24_64bits.tar.gz'] +sources = ['%(name)s.%(version_minor)s_64bits.tar.gz'] checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] skipsteps = ['configure'] From 94e203dcc8654818dc7bc1e2dae2de5358a9260e Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 10 Nov 2021 15:24:09 +0100 Subject: [PATCH 068/528] Update easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb --- .../h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb index 66d8b4e92b2..ad341bc26e5 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -34,6 +34,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], }), ] From f15e9bd3d43d581497c0c9628c679a72565f6a49 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 22:02:35 +1050 Subject: [PATCH 069/528] deps + --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 47cd3dce2d2..d9470e12178 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -10,7 +10,9 @@ version = '24.2.0' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Magdoll/cDNA_Cupcake' -description = "cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data." +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" toolchain = {'name': 'foss', 'version': '2020a'} @@ -23,13 +25,14 @@ dependencies = [ ('SciPy-bundle', '2020.03', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), + ('bcbio-gff', '0.6.6', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('Pysam', '0.16.0.1'), ] -download_dep_fail = True +download_dep_fail = False use_pip = True -options = {'modulename': 'cupcake'} - sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, @@ -42,4 +45,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +options = {'modulename': 'cupcake'} + moduleclass = 'bio' From 86fd039a1cbb3184580adce0952be7c298d946ed Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 11 Nov 2021 17:59:40 +0100 Subject: [PATCH 070/528] add patch for Qt5-5.15.2-GCCcore-11.2.0.eb --- .../q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 + .../q/Qt5/Qt5-5.15.2_fix-gcc11.patch | 139 ++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 0ae4b2b7fe1..52359f23f25 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -20,12 +20,14 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.2_fix-gcc11.patch', ] checksums = [ '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch + '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976', # Qt5-5.15.2_fix-gcc11.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch new file mode 100644 index 00000000000..0a9ec1a4a99 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch @@ -0,0 +1,139 @@ +# Qt 5.15.2 build fixes for GCC 11 +# +# Upstream patches: +# https://code.qt.io/cgit/qt/qtbase.git/commit/?id=813a928c7c3cf986 +# https://code.qt.io/cgit/qt/qtbase.git/commit/?id=9c56d4da2ff631a8 +# https://code.qt.io/cgit/qt/qtdeclarative.git/commit/?id=367293b18ab0d0a0 +# +# Third-party software patches (taken from Fedora): +# https://src.fedoraproject.org/rpms/qt5-qtwebengine/blob/rawhide/f/qtwebengine-gcc11.patch +# +diff -Nrup a/qtbase/src/corelib/global/qendian.h b/qtbase/src/corelib/global/qendian.h +--- a/qtbase/src/corelib/global/qendian.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/global/qendian.h 2021-06-21 18:02:01.741899258 +0200 +@@ -1,7 +1,7 @@ + /**************************************************************************** + ** +-** Copyright (C) 2016 The Qt Company Ltd. +-** Copyright (C) 2016 Intel Corporation. ++** Copyright (C) 2021 The Qt Company Ltd. ++** Copyright (C) 2021 Intel Corporation. + ** Contact: https://www.qt.io/licensing/ + ** + ** This file is part of the QtCore module of the Qt Toolkit. +@@ -44,6 +44,8 @@ + #include + #include + ++#include ++ + // include stdlib.h and hope that it defines __GLIBC__ for glibc-based systems + #include + #include +diff -Nrup a/qtbase/src/corelib/global/qfloat16.h b/qtbase/src/corelib/global/qfloat16.h +--- a/qtbase/src/corelib/global/qfloat16.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/global/qfloat16.h 2021-06-21 18:02:17.409709370 +0200 +@@ -43,6 +43,7 @@ + + #include + #include ++#include + #include + + #if defined(QT_COMPILER_SUPPORTS_F16C) && defined(__AVX2__) && !defined(__F16C__) +diff -Nrup a/qtbase/src/corelib/text/qbytearraymatcher.h b/qtbase/src/corelib/text/qbytearraymatcher.h +--- a/qtbase/src/corelib/text/qbytearraymatcher.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/text/qbytearraymatcher.h 2021-06-21 18:13:45.885352546 +0200 +@@ -42,6 +42,8 @@ + + #include + ++#include ++ + QT_BEGIN_NAMESPACE + + +diff -Nrup a/qtbase/src/corelib/tools/qsharedpointer_impl.h b/qtbase/src/corelib/tools/qsharedpointer_impl.h +--- a/qtbase/src/corelib/tools/qsharedpointer_impl.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/tools/qsharedpointer_impl.h 2021-06-21 18:13:45.885352546 +0200 +@@ -155,9 +155,6 @@ namespace QtSharedPointer { + #endif + inline void checkQObjectShared(...) { } + inline void setQObjectShared(...) { } +- +- inline void operator delete(void *ptr) { ::operator delete(ptr); } +- inline void operator delete(void *, void *) { } + }; + // sizeof(ExternalRefCountData) = 12 (32-bit) / 16 (64-bit) + +diff -Nrup a/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp b/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp +--- a/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp 2021-06-21 18:13:45.885352546 +0200 +@@ -698,7 +698,7 @@ void QXcbWindow::show() + if (isTransient(window())) { + const QWindow *tp = window()->transientParent(); + if (tp && tp->handle()) +- transientXcbParent = static_cast(tp->handle())->winId(); ++ transientXcbParent = tp->handle()->winId(); + // Default to client leader if there is no transient parent, else modal dialogs can + // be hidden by their parents. + if (!transientXcbParent) +diff -Nrup a/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h b/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h +--- a/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h 2020-10-27 09:02:12.000000000 +0100 ++++ b/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h 2021-06-22 09:35:22.877912946 +0200 +@@ -48,6 +48,7 @@ + #include + + #include ++#include + #include + + // +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc 2021-06-22 12:05:40.736177321 +0200 +@@ -14,9 +14,9 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/containers/string_pool.h" + +-#include + + #include "perfetto/base/logging.h" + #include "perfetto/ext/base/utils.h" +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc 2021-06-22 12:06:05.087880649 +0200 +@@ -14,6 +14,7 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/db/column.h" + + #include "src/trace_processor/db/compare.h" +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc 2021-06-22 12:06:28.911590412 +0200 +@@ -14,6 +14,8 @@ + * limitations under the License. + */ + ++#include ++ + #include "src/trace_processor/importers/proto/heap_graph_walker.h" + #include "perfetto/base/logging.h" + +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc 2021-06-22 12:06:52.631301445 +0200 +@@ -14,6 +14,7 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/types/variadic.h" + + namespace perfetto { From 9b534cdf6880cd0f73f468af3621dafb76b6c88f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 13:02:11 +1050 Subject: [PATCH 071/528] deps + --- .../MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index f484f3c9d9b..d2b2b7fdc2b 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -27,13 +27,18 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('Pysam', '0.16.0.1'), + ('DendroPy', '4.4.0'), + ('CMSeq', '1.0.3', versionsuffix), + ('biom-format', '2.1.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), ] use_pip = True -use_pip_for_deps = True -sanity_pip_check = True download_dep_fail = False +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], 'dirs': ['bin', 'lib'], From e6dd0a41b31f37d41002fcff583e52aa6519a8dc Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 13 Nov 2021 21:13:30 +0100 Subject: [PATCH 072/528] update Qt5-5.15.2-GCCcore-11.2.0.eb: Downgrade to Python/2.7.18-bare as Python2 is a build dependecy for Qt5WebEngine --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 52359f23f25..2d43727ea14 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -38,7 +38,8 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.10.2'), - ('Python', '3.9.6', '-bare'), + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), ('re2c', '2.2'), ] From d5c0cc806382aa583dd7edd9b10028534ec6b8a9 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 12:59:23 +0100 Subject: [PATCH 073/528] Added QCG-PilotJob --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb | 25 +++++++ .../p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb | 28 ++++++++ .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 68 +++++++++++++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2f09b3ca33d --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..de5166f57a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '22.3.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eddc033e716f8c91c6a2112f0a8ebc5e00532b4a6ae1eb0ccc48e027f9c671c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('ZeroMQ', '4.3.4'), +] + +options = {'modulename': 'zmq'} + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb new file mode 100644 index 00000000000..88913eb6d99 --- /dev/null +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.12.3' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = """A python service for easy execution of many tasks inside a single allocation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyZMQ', '22.3.0'), + ('Kaleido', '0.2.1'), + ('plotly.py', '5.1.0'), +] + +download_dep_fail = True +use_pip = True + +# Disable sanity check because `zmq` has an invalid version. +sanity_pip_check = False + +exts_list = [ + ('zmq', '0.0.0', { + 'sources': [{ + 'filename': 'zmq-0.0.0.tar.gz', + 'download_filename': 'zmq.tar.gz', + }], + 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], + }), + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('statsmodels', '0.13.0', { + 'checksums': ['f2efc02011b7240a9e851acd76ab81150a07d35c97021cb0517887539a328f8a'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.21', { + 'checksums': ['27f13ff4e4850fe8f860b77414c7880f67c6158076a7b099062cc8570f1562e5'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/core', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/cmds', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/executor_api', + }), +] + +moduleclass = 'tools' From 62855477cf93c2b7f6ceb1699826331fbdc077f8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 20:58:17 +0100 Subject: [PATCH 074/528] Removed download_dep_fail and sanity_pip_check --- easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index 88913eb6d99..c7e423450ce 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -16,12 +16,8 @@ dependencies = [ ('plotly.py', '5.1.0'), ] -download_dep_fail = True use_pip = True -# Disable sanity check because `zmq` has an invalid version. -sanity_pip_check = False - exts_list = [ ('zmq', '0.0.0', { 'sources': [{ From a346f8a0dca4baf2a442bbf1ab37b4be2f82adad Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 21:52:34 +0100 Subject: [PATCH 075/528] Cleaning --- .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index c7e423450ce..abc5610df44 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -20,10 +20,6 @@ use_pip = True exts_list = [ ('zmq', '0.0.0', { - 'sources': [{ - 'filename': 'zmq-0.0.0.tar.gz', - 'download_filename': 'zmq.tar.gz', - }], 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], }), ('patsy', '0.5.2', { @@ -42,21 +38,21 @@ exts_list = [ 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/core', }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/cmds', }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/executor_api', }), ] From 1642bb9f8ff6b64a9225d6bdf5ee52c39bdc54a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 19 Nov 2021 11:45:45 +0100 Subject: [PATCH 076/528] adding easyconfigs: Schrodinger-2021-4.eb --- .../s/Schrodinger/Schrodinger-2021-4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb new file mode 100644 index 00000000000..ba0edb4190a --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb @@ -0,0 +1,31 @@ +easyblock='PackedBinary' + +name = 'Schrodinger' +version = '2021-4' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['555eb6e2da507463870e9b15ec89a709daf4510871e192d556b8659430d0fa18'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond', 'maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From ccfa4a2b5729c22c8aee6c29f80981fb07c67603 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 1 Dec 2021 13:22:04 +0200 Subject: [PATCH 077/528] adding easyconfigs: FMPy-0.3.2-foss-2021a.eb, PyOpenGL-3.1.5-GCCcore-10.3.0.eb, PyQtGraph-0.12.3-foss-2021a.eb, FMPy-0.3.2-foss-2021a.eb --- .../f/FMPy/FMPy-0.3.2-foss-2021a.eb | 81 +++++++++++++++++++ .../PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb | 43 ++++++++++ .../PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb | 30 +++++++ 3 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb new file mode 100644 index 00000000000..4e8249a47d2 --- /dev/null +++ b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb @@ -0,0 +1,81 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'FMPy' +version = '0.3.2' + +homepage = 'https://github.com/CATIA-Systems/FMPy' +description = "FMPy is a free Python library to simulate Functional Mock-up Units (FMUs)." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('lxml', '4.6.3'), + ('SciPy-bundle', '2021.05'), + ('dask', '2021.9.1'), + ('PyQt5', '5.15.4'), + ('PyQtGraph', '0.12.3'), + ('IPython', '7.25.0'), + ('plotly.py', '5.1.0'), + ('Flask', '1.1.4'), + ('Brotli', '1.0.9'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('lark-parser', '0.12.0', { + 'modulename': 'lark', + 'checksums': ['15967db1f1214013dca65b1180745047b9be457d73da224fcda3d9dd4e96a138'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('dash', '2.0.0', { + 'checksums': ['29277c24e2f795b069cb102ce1ab0cd3ad5cf9d3b4fd16c03da9671a5eea28a4'], + }), + ('dash-bootstrap-components', '1.0.0', { + 'source_tmpl': 'dash-bootstrap-components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-bootstrap-components/'], + 'checksums': ['498164307c3a05b295fcf92cc4e39a91f6eed5be6d960b03081feb8f791adf94'], + }), + ('dash-core-components', '2.0.0', { + 'source_tmpl': 'dash_core_components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-core-components/'], + 'checksums': ['c6733874af975e552f95a1398a16c2ee7df14ce43fa60bb3718a3c6e0b63ffee'], + }), + ('dash-html-components', '2.0.0', { + 'source_tmpl': 'dash_html_components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-html-components/'], + 'checksums': ['8703a601080f02619a6390998e0b3da4a5daabe97a1fd7a9cebc09d015f26e50'], + }), + ('dash-table', '5.0.0', { + 'source_tmpl': 'dash_table-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-table/'], + 'checksums': ['18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308'], + }), + ('Flask-Compress', '1.10.1', { + 'checksums': ['28352387efbbe772cfb307570019f81957a13ff718d994a9125fa705efb73680'], + }), + ('idna', '2.8', { + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/CATIA-Systems/FMPy/archive/'], + 'use_pip_extras': 'complete', + 'checksums': ['d534d819972048557a44f797b1e2247961d871540b9dfae52e88ce6e49867296'], + }), +] + +sanity_check_commands = ["fmpy --help"] + +sanity_check_paths = { + 'files': ['bin/fmpy', 'bin/renderer'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2081c55d0b4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# Updated:: Denis Kristak (INUITS) +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.5' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb new file mode 100644 index 00000000000..fef424d65b3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb @@ -0,0 +1,30 @@ +# updated: Denis Kristak +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +name = 'PyQtGraph' +version = '0.12.3' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['243df67ce5461e7f44afa19e351dc4f1bf08a231925b7cb4a2f232c6d71e8957'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyQt5', '5.15.4'), + ('PyOpenGL', '3.1.5'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' From 75b12676a789e575819058f38a4db0cd104d34e4 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:04:37 +0100 Subject: [PATCH 078/528] Added patch to rename zmq with pyzmq --- .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 10 ++++++---- .../QCGPilotJob-0.12.3_rename_zmq.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index abc5610df44..9402d6b7e44 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -17,11 +17,9 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ - ('zmq', '0.0.0', { - 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], - }), ('patsy', '0.5.2', { 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], }), @@ -40,7 +38,11 @@ exts_list = [ ('qcg', '0.12.3', { 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], + 'patches': ['QCGPilotJob-0.12.3_rename_zmq.patch'], + 'checksums': [ + '9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966', # v0.12.3.tar.gz + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCGPilotJob-0.12.3_rename_zmq.patch + ], 'start_dir': 'components/core', }), ('qcg', '0.12.3', { diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch new file mode 100644 index 00000000000..3fa5595dadb --- /dev/null +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch @@ -0,0 +1,14 @@ +# Replace zmq with pyzmq +# Author: maxim-masterov (SURF) +diff -Nru QCG-PilotJob-0.12.3.orig/components/core/setup.py QCG-PilotJob-0.12.3/components/core/setup.py +--- QCG-PilotJob-0.12.3.orig/components/core/setup.py 2021-12-02 13:33:02.564287000 +0100 ++++ QCG-PilotJob-0.12.3/components/core/setup.py 2021-12-02 15:00:08.997343000 +0100 +@@ -27,7 +27,7 @@ + long_description_content_type="text/markdown", + + install_requires=[ +- "zmq", ++ "pyzmq", + "click", + "psutil", + ], From 8dbd70aeb4a6dbed986fcd2ee37a749e6f76361b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:35:08 +0100 Subject: [PATCH 079/528] Renamed easyconfig --- .../{QCGPilotJob-0.12.3.eb => QCGPilotJob-0.12.3-foss-2021a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3.eb => QCGPilotJob-0.12.3-foss-2021a.eb} (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb rename to easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb From 9bfd923aa7f13c3f1cdb453bf5d2118b3b597239 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:48:16 +0100 Subject: [PATCH 080/528] Renamed easycinfig --- ...Job-0.12.3-foss-2021a.eb => QCG-PilotJob-0.12.3-foss-2021a.eb} | 0 ...12.3_rename_zmq.patch => QCG-PilotJob-0.12.3_rename_zmq.patch} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3-foss-2021a.eb => QCG-PilotJob-0.12.3-foss-2021a.eb} (100%) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3_rename_zmq.patch => QCG-PilotJob-0.12.3_rename_zmq.patch} (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb rename to easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch rename to easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch From ee5ade12111a7071b749c9b6a34445049ece9e4e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 19:02:59 +0100 Subject: [PATCH 081/528] Renamed folder --- .../QCG-PilotJob-0.12.3-foss-2021a.eb | 0 .../QCG-PilotJob-0.12.3_rename_zmq.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/{QCGPilotJob => QCG-PilotJob}/QCG-PilotJob-0.12.3-foss-2021a.eb (100%) rename easybuild/easyconfigs/q/{QCGPilotJob => QCG-PilotJob}/QCG-PilotJob-0.12.3_rename_zmq.patch (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb rename to easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch rename to easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch From 902cbd3f38d79fb8069bb286b985763466348314 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 19:15:43 +0100 Subject: [PATCH 082/528] Fixed patch name --- .../q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb index 9402d6b7e44..e15fca04e5d 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb @@ -38,10 +38,10 @@ exts_list = [ ('qcg', '0.12.3', { 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'patches': ['QCGPilotJob-0.12.3_rename_zmq.patch'], + 'patches': ['QCG-PilotJob-0.12.3_rename_zmq.patch'], 'checksums': [ '9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966', # v0.12.3.tar.gz - '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCGPilotJob-0.12.3_rename_zmq.patch + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCG-PilotJob-0.12.3_rename_zmq.patch ], 'start_dir': 'components/core', }), From 69a3a01190e72fe6bcc3bf21abe8ca8afe9e4ca9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 2 Dec 2021 18:31:04 +0000 Subject: [PATCH 083/528] adding easyconfigs: FreeSurfer-7.2.0-ubuntu18_amd64.eb, FreeSurfer-7.2.0-centos7_x86_64.eb, FreeSurfer-7.2.0-centos8_x86_64.eb --- .../FreeSurfer-7.2.0-centos7_x86_64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.2.0-centos8_x86_64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.2.0-ubuntu18_amd64.eb | 33 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb new file mode 100644 index 00000000000..c918d56dab9 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-centos7_x86_64-7.2.0.tar.gz + '4cca78602f898bf633428b9d82cbb9b07e3ab97a86c620122050803779c86d62', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb new file mode 100644 index 00000000000..22a5572078f --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-centos8_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-centos8_x86_64-7.2.0.tar.gz + '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', + '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb new file mode 100644 index 00000000000..18fc67d8672 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-ubuntu18_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz + 'e0cbd55809359ce7f8019d6e8794524cd9f182ab9d1a151644d6ccd3ee582cd2', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From 57956887f87b627239a921f46c2020705be38411 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 4 Dec 2021 16:35:07 +0000 Subject: [PATCH 084/528] Checksums corrected --- .../f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb index 22a5572078f..5fc7c985195 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb @@ -20,8 +20,8 @@ sources = [ ] checksums = [ # freesurfer-linux-centos8_x86_64-7.2.0.tar.gz - '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', - '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', # runtime2014bLinux.tar.gz + '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] From 2b33505ae6676421a8941743c3fc47495978bef2 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 6 Dec 2021 12:24:04 +0100 Subject: [PATCH 085/528] easyconfigs for dune-core and dune-fem in foss/2020b --- .../dune-core-2.8.0.post1-foss-2020b.eb | 56 +++++++++++++++ .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 71 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb new file mode 100644 index 00000000000..3c4f56daebe --- /dev/null +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'dune-core' +version = '2.8.0.post1' + +homepage = "https://www.dune-project.org/groups/core/" +description = """The Dune core modules build the stable basis of Dune. +They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. +These modules build the foundation for higher-level components. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('CMake', '3.18.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('portalocker', '2.3.2', { + 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + }), + ('dune-common', version, { + 'modulename': 'dune.common', + 'checksums': ['b6736c69d5213688405bc1d953ac907c1440ecda1174c0cf08bf6cf69ee585a1'], + }), + ('dune-geometry', version, { + 'modulename': 'dune.geometry', + 'checksums': ['7fc655c42fde485bc563d362d9309db332acd08229df2ad215fa0fd292e18a54'], + }), + ('dune-grid', version, { + 'modulename': 'dune.grid', + 'checksums': ['1faf909dba2a590086aa0a2e5926905fcbbe3521e9d920359c984ab496a3c5fb'], + }), + ('dune-localfunctions', version, { + 'modulename': 'dune.localfunctions', + 'checksums': ['d19cb354cbce72654220228613f53ed1be3b960718d8738523b987da6d108406'], + }), + ('dune-istl', version, { + 'modulename': 'dune.istl', + 'checksums': ['0227acaf6b93700036403c3fe8312c00b33edc9dc09d89b295768cbe84eff507'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb new file mode 100644 index 00000000000..20d66b9fdd7 --- /dev/null +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'dune-fem' +version = '2.8.0.6' + +homepage = "https://www.dune-project.org/modules/dune-fem/" +description = """DUNE-FEM is a discretization module based on DUNE containing all +the building blocks required to implement efficient solvers for a wide range +of (systems of non linear) partial differential equations. DUNE-FEM can also +be used through an extensive Python interface which brings all +components of DUNE-FEM and the DUNE core modules to Python. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PETSc', '3.14.4'), + ('CMake', '3.18.4'), + ('dune-core', '2.8.0.post1'), + ('matplotlib', '3.3.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('fenics-ufl', '2019.1.0', { + 'modulename': 'ufl', + 'checksums': ['f778cb914f0fe57be76ad288a9209c1f4034a65692e13907171d994a4747bf81'], + }), + ('dune-alugrid', '2.8.0.post1', { + 'modulename': 'dune.alugrid', + 'checksums': ['3ee0ecdc19add77535c211c60058bf28162f9ad3c54b8b3b2bfcafc4d6269c55'], + }), + ('dune-spgrid', '2.8.0.post1', { + 'modulename': 'dune.spgrid', + 'checksums': ['9c6047d5672aabef1b39e9604f03611a1097070935e3c2b1224f69f8758fa336'], + }), + ('dune-polygongrid', '2.8.0.post1', { + 'modulename': 'dune.polygongrid', + 'checksums': ['a1b3dd301a403db6ea0b0a2d9e267b292dd6c5b3d12801f5154890bd4b6d63a8'], + }), + (name, version, { + 'modulename': 'dune.fem', + 'checksums': ['85151aa6fe54d14ae7cee12feff90afc580e0e41f5636bf51a6fbb2b9921bf10'], + }), + ('dune-fem-dg', version, { + 'modulename': 'dune.femdg', + 'checksums': ['bb81fdaf0ba0f59915dca8080d82f2c6b1d2ad98cd51cf8548b0c96d88adebb0'], + }), + ('triangle', '20200424', { + 'checksums': ['fc207641f8f39986f7d2bee1b91688a588cd235d2e67777422f94e61fece27e9'], + }), + ('dune-vem', version, { + 'modulename': 'dune.vem', + 'checksums': ['452145b85f2755cda24aa683efd4cc6c90fd49af395333dd766fb6cf479f969b'], + }), +] + + + +moduleclass = 'math' From eb46d53772d0d9cebdf84f20de52ce633c39d553 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 14:37:38 +0100 Subject: [PATCH 086/528] Updated matplotlib version in dune-fem --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 20d66b9fdd7..fa6041e9808 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('PETSc', '3.14.4'), ('CMake', '3.18.4'), ('dune-core', '2.8.0.post1'), - ('matplotlib', '3.3.4'), + ('matplotlib', '3.3.3'), ] use_pip = True From eb76081339ce347cf3d4a8479e34fc27ffebf6d7 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 15:14:19 +0100 Subject: [PATCH 087/528] removed unwanted whitespace in dune-fem configuration --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index fa6041e9808..6d875c7c146 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -66,6 +66,4 @@ exts_list = [ }), ] - - moduleclass = 'math' From c29f3d1095cddbb63407e2adbe33887a1b9e2770 Mon Sep 17 00:00:00 2001 From: eb-test Date: Wed, 8 Dec 2021 13:22:54 +0100 Subject: [PATCH 088/528] adding easyconfigs: Arrow-6.0.1-foss-2021a.eb, LMfit-1.0.3-foss-2021a.eb, Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb, plotly.py-4.14.3-GCCcore-10.3.0.eb, boost_histogram-1.2.1-foss-2021a.eb, Zgoubi-6.0.2-GCCcore-10.3.0.eb, georges-2019.2-foss-2021a-Python-3.9.5.eb --- .../a/Arrow/Arrow-6.0.1-foss-2021a.eb | 59 +++++++++++++++++++ .../boost_histogram-1.2.1-foss-2021a.eb | 28 +++++++++ .../georges-2019.2-foss-2021a-Python-3.9.5.eb | 46 +++++++++++++++ .../l/LMfit/LMfit-1.0.3-foss-2021a.eb | 33 +++++++++++ .../Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb | 28 +++++++++ .../plotly.py-4.14.3-GCCcore-10.3.0.eb | 30 ++++++++++ .../z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 28 +++++++++ 7 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb new file mode 100644 index 00000000000..425e7dbb2d6 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '6.0.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['3786b3d2df954d078b3e68f98d2e5aecbaa3fa2accf075d7a3a13c187b9c5294'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..5a0bffca63f --- /dev/null +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'boost_histogram' +version = '1.2.1' + +homepage = 'https://pypi.org/project/boost-histogram/' +description = """This is one of the fastest libraries for histogramming, +while still providing the power of a full histogram object""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('pybind11', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..8e5f7b94288 --- /dev/null +++ b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'georges' +version = '2019.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ULB-Metronu/georges' +description = """Georges the lemur opinionated particle accelerator modeling Python package. +Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('LMfit', '1.0.3'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('m2r', '0.2.1', { + 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], + 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb new file mode 100644 index 00000000000..c44b966b7d7 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.25', { + 'checksums': ['bea22b7d8fa16bcba95ebc72052ae5d8ca97114c9959bb47f8b8eebf30e4342f'], + }), + ('uncertainties', '3.1.6', { + 'checksums': ['7c4db5aaafd227e95485b61fba5d235dc8133aeecd98f8fc1224c038ce063e2d'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb new file mode 100644 index 00000000000..e695e3bff9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.17' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f4d0caa713239e6847a7c6eefe2427358566451fe56497d533f21fb590a3f313'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6cfb8cf4ced --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '4.14.3' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [('Python', '3.9.5')] + +use_pip = True + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3ca79813105 --- /dev/null +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Zgoubi' +version = '6.0.2' + +homepage = 'https://zgoubi.sourceforge.io' +description = """Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulations. +It can simulate beam dynamics in a large variety of machines and optical systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] +sources = ['%(version)s/zgoubi-%(version)s.tar.bz2'] +checksums = ['0b0f3d28496edbf7be868c24b0c927b7f1bc88cc29df9c235d9b28dc933489e0'] + +prebuildopts = 'cp Makefile_zgoubi_gfortran Makefile &&' +prebuildopts += "sed -i '/guide/d' Makefile &&" + +buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' + +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/zgoubi", "bin/zpop"], + 'dirs': [], +} + +moduleclass = 'phys' From 14bb239caa5fa00e6d899e458c9b6bd5806da774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Dec 2021 22:12:40 +0100 Subject: [PATCH 089/528] adding easyconfigs: SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb --- .../SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..9fa4d8fd8bb --- /dev/null +++ b/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'SCopeLoomR' +local_commit = '99726f5' +version = '0.13.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/aertslab/SCopeLoomR' +description = """An R package (compatible with SCope) to create generic .loom files and extend them with other data +e.g.: SCENIC regulons, Seurat clusters and markers, ...""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), + ('HDF5', '1.12.1'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + (name, version, { + 'source_urls': ['https://github.com/aertslab/%(name)s/archive'], + 'sources': [{'download_filename': '99726f5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['02c8d331b5808c6fed09161f5208dd3655b41588b920c50be429f65719abf0cd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'tools' From 12f272f3fecda3ac50a6abae703bde47913952d5 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 8 Dec 2021 22:20:43 +0100 Subject: [PATCH 090/528] Adding PyOpenCL for fosscuda/2020b --- .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 00000000000..0f033662e72 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' From 1408863d50688519a35e4c00f718d6801766384f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 9 Dec 2021 08:53:20 +0100 Subject: [PATCH 091/528] adding easyconfigs: DIAMOND-2.0.13-GCC-10.3.0.eb --- .../d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb new file mode 100644 index 00000000000..95476f692b1 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.13' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b79c3a01913999dfa2543f4dd7a3494397a8723ea587207c14683b24e57eac1'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.20.1') +] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["diamond help"] + +moduleclass = 'bio' From b48bba970ac0378987e7840fdacebe8a6b1d7eda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 9 Dec 2021 09:11:45 +0100 Subject: [PATCH 092/528] adding easyconfigs: GTDB-Tk-1.7.0-foss-2021a.eb, FastTree-2.1.11-GCCcore-10.3.0.eb --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 35 +++++++++++++++ .../g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb | 43 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e210cab5b2b --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'https://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.36.1')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb new file mode 100644 index 00000000000..05e89644664 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.61.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 5124b43b6b3f6c6a5ff05d387392b06ef70d7abc Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 9 Dec 2021 09:06:58 +0000 Subject: [PATCH 093/528] adding easyconfigs: ORCA-5.0.2-gompi-2021a-static.eb, ORCA-5.0.2-gompi-2021a.eb --- .../o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb | 29 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.2-gompi-2021a.eb | 23 +++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb new file mode 100644 index 00000000000..fd53dc9c626 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb @@ -0,0 +1,29 @@ +name = 'ORCA' +version = '5.0.2' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 4)] +checksums = [ + # orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz + '7623ae43a7d02a36f890a3826e0d021d634addb8e1b2598feb7f9b29d8a3f935', + # orca_5_0_2_linux_x86-64_openmpi411_part2.tar.xz + '905b427a721554a0037986494473a91daa4a0b182dcfbb92fe5d2abccc68df2c', + # orca_5_0_2_linux_x86-64_openmpi411_part3.tar.xz + 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb new file mode 100644 index 00000000000..c4ee43cd9be --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_2_linux_x86-64_shared_openmpi411.tar.xz + '3a26a1a5fbc69e7dca0192237b5e16b69886df31751ae59f7396461428aeee96', +] + +moduleclass = 'chem' From b49293bf9a08997a8863e4b987a4a830ac2efeeb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 9 Dec 2021 13:45:08 +0100 Subject: [PATCH 094/528] {chem}[foss/2020b] yaff 1.6.0 --- .../h/h5py/h5py-2.10.0-foss-2020b.eb | 35 +++++++++++++++ .../m/molmod/molmod-1.4.8-foss-2020b.eb | 34 +++++++++++++++ .../y/yaff/yaff-1.6.0-foss-2020b.eb | 43 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb new file mode 100644 index 00000000000..29f06c60e0d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['h5py-%(version)s_avoid-mpi-init.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch +] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb new file mode 100644 index 00000000000..55945818bbf --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb new file mode 100644 index 00000000000..e86af8d99d0 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive Slurm session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this as non-interactive Slurm job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + # Needs h5py version 2 + ('h5py', '2.10.0'), + ('molmod', '1.4.8'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +moduleclass = 'chem' From 74c7b759b9c8dad6cc690dc1c6a8900258a87a5c Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Fri, 10 Dec 2021 06:28:27 +0000 Subject: [PATCH 095/528] Strip redundant ORCA top-level directories when unpacking --- easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb index fd53dc9c626..ca35b29f949 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb @@ -26,4 +26,8 @@ checksums = [ 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', ] +# The 5.0.2-static tarballs have redundant top-level directory names names that +# need to be stripped away. +unpack_options = '--strip-components=1' + moduleclass = 'chem' From aa05bae9c7c951ec66fcb422f9948d6a231349c8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Dec 2021 11:34:43 +0100 Subject: [PATCH 096/528] adding easyconfigs: Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb --- .../Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..c66061a04a9 --- /dev/null +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Binary' + +name = 'Rgurobi' +version = '9.5.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.gurobi.com' +description = """Gurobi Optimizer %(version_major_minor)s interface""" +# NOTE not in the license list of EB +# software_license = 'LGPL-2.1' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['gurobi%(version)s_linux64.tar.gz'] +checksums = ['bb542e5a5d1685f6e364eaf05ea6c5572485ffc37a2245169cf3cb40288bc29e'] + +dependencies = [ + ('R', '4.1.0'), + ('Gurobi', version), +] + +extract_sources = True +install_cmd = 'R CMD INSTALL R/gurobi_*.tar.gz --library=%(installdir)s --no-clean-on-error' + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['gurobi'], +} + +moduleclass = 'math' From fb49404b8a1d7f20270f8c1a33bfb8b483c8edac Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 11:43:35 +0100 Subject: [PATCH 097/528] bundle h5py to yaff --- .../h/h5py/h5py-2.10.0-foss-2020b.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb deleted file mode 100644 index 29f06c60e0d..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', '-python')] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('HDF5', '1.10.7'), -] - -use_pip = True -sanity_pip_check = True -download_dep_fail = True - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' From 2859be8f5d7b5f0e9a5faae4a5143e0f591f8d65 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 11:44:34 +0100 Subject: [PATCH 098/528] bundle h5py to yaff v2 --- .../y/yaff/yaff-1.6.0-foss-2020b.eb | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e86af8d99d0..e7103d4a5c0 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -8,7 +8,7 @@ # If you submit this as non-interactive Slurm job, it will build just fine. # Possibly root cause: https://github.com/h5py/h5py/issues/917 # -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'yaff' version = '1.6.0' @@ -18,15 +18,12 @@ description = """Yaff stands for 'Yet another force field'. It is a pythonic for toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - # Needs h5py version 2 - ('h5py', '2.10.0'), + ('HDF5', '1.10.7'), ('molmod', '1.4.8'), ] @@ -34,10 +31,25 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + 'source_urls': ['https://pypi.python.org/packages/source/h/h5py'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + }), + (name, version, { + 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], + 'runtest': local_runtest, + 'checksums': ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'], + }), +] -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" moduleclass = 'chem' From 81d553ef373e24e81d2533f2c6cca13bb98c388f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Dec 2021 21:41:04 +1050 Subject: [PATCH 099/528] adding easyconfigs: cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb --- ..._Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..02a39c41144 --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,50 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '26.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05', versionsuffix), + ('Biopython', '1.79', versionsuffix), + ('bx-python', '0.8.11', versionsuffix), + ('bcbio-gff', '0.6.7', versionsuffix), + ('scikit-learn', '0.24.2', versionsuffix), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = False +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'cupcake'} + +moduleclass = 'bio' From 2cff19ec64c9ce00f8c68830f88906a0e30bd117 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 12:04:29 +0100 Subject: [PATCH 100/528] Add h5py pathc file --- .../y/yaff/h5py-2.10.0_avoid-mpi-init.patch | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch diff --git a/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch b/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch new file mode 100644 index 00000000000..98034776400 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch @@ -0,0 +1,85 @@ +avoid that 'import h5py' triggers MPI_Init via mpi4py + +backported to h5py 2.10.0 from https://github.com/h5py/h5py/pull/1552 by Kenneth Hoste (HPC-UGent) + +diff -ru h5py-2.10.0.orig/h5py/api_types_ext.pxd h5py-2.10.0/h5py/api_types_ext.pxd +--- h5py-2.10.0.orig/h5py/api_types_ext.pxd 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/api_types_ext.pxd 2020-05-25 19:30:30.000000000 +0200 +@@ -12,7 +12,7 @@ + include 'config.pxi' + + IF MPI: +- from mpi4py.MPI cimport MPI_Comm, MPI_Info, Comm, Info ++ from mpi4py.libmpi cimport MPI_Comm, MPI_Info + + cdef extern from "stdlib.h": + ctypedef long size_t +@@ -52,6 +52,7 @@ + cdef extern from "Python.h": + ctypedef void PyObject + ctypedef ssize_t Py_ssize_t ++ ctypedef size_t Py_uintptr_t + + PyObject* PyErr_Occurred() + void PyErr_SetString(object type, char *message) +diff -ru h5py-2.10.0.orig/h5py/h5p.pyx h5py-2.10.0/h5py/h5p.pyx +--- h5py-2.10.0.orig/h5py/h5p.pyx 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/h5p.pyx 2020-05-25 19:33:24.000000000 +0200 +@@ -17,6 +17,7 @@ + from cpython.buffer cimport PyObject_CheckBuffer, \ + PyObject_GetBuffer, PyBuffer_Release, \ + PyBUF_SIMPLE ++from cpython.long cimport PyLong_AsVoidPtr + + from utils cimport require_tuple, convert_dims, convert_tuple, \ + emalloc, efree, \ +@@ -1161,7 +1162,7 @@ + + IF MPI: + @with_phil +- def set_fapl_mpio(self, Comm comm not None, Info info not None): ++ def set_fapl_mpio(self, comm, info): + """ (Comm comm, Info info) + + Set MPI-I/O Parallel HDF5 driver. +@@ -1169,7 +1170,12 @@ + Comm: An mpi4py.MPI.Comm instance + Info: An mpi4py.MPI.Info instance + """ +- H5Pset_fapl_mpio(self.id, comm.ob_mpi, info.ob_mpi) ++ from mpi4py.MPI import Comm, Info, _handleof ++ assert isinstance(comm, Comm) ++ assert isinstance(info, Info) ++ cdef Py_uintptr_t _comm = _handleof(comm) ++ cdef Py_uintptr_t _info = _handleof(info) ++ H5Pset_fapl_mpio(self.id, _comm, _info) + + + @with_phil +@@ -1183,20 +1189,22 @@ + """ + cdef MPI_Comm comm + cdef MPI_Info info ++ from mpi4py.MPI import Comm, Info, _addressof + + H5Pget_fapl_mpio(self.id, &comm, &info) + pycomm = Comm() +- pyinfo = Info() +- MPI_Comm_dup(comm, &pycomm.ob_mpi) +- MPI_Info_dup(info, &pyinfo.ob_mpi) ++ MPI_Comm_dup(comm, PyLong_AsVoidPtr(_addressof(pycomm))) + MPI_Comm_free(&comm) ++ ++ pyinfo = Info() ++ MPI_Info_dup(info, PyLong_AsVoidPtr(_addressof(pyinfo))) + MPI_Info_free(&info) + + return (pycomm, pyinfo) + + + @with_phil +- def set_fapl_mpiposix(self, Comm comm not None, bint use_gpfs_hints=0): ++ def set_fapl_mpiposix(self, comm, bint use_gpfs_hints=0): + """ Obsolete. + """ + raise RuntimeError("MPI-POSIX driver is broken; removed in h5py 2.3.1") From 08c44bc951b22dba8e0354c407d8e75593e18b8b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 12:21:21 +0100 Subject: [PATCH 101/528] remove download_dep_fail --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e7103d4a5c0..229465a24ee 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -28,7 +28,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " From 69bc26539726bacf02d69e0b3e19c881cee1b375 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 10 Dec 2021 11:29:37 +0000 Subject: [PATCH 102/528] adding easyconfigs: carma-2.01-foss-2019b.eb --- .../c/carma/carma-2.01-foss-2019b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb new file mode 100644 index 00000000000..40bf7dc47da --- /dev/null +++ b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb @@ -0,0 +1,34 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco +# License:: GPL-v3.0 +# # + +easyblock = 'Tarball' + +name = 'carma' +version = '2.01' + +homepage = 'http://utopia.duth.gr/~glykos/Carma.html' +description = """carma - A molecular dynamics analysis program""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['http://utopia.duth.gr/~glykos/progs/'] +sources = ['%(name)s.tar.gz'] +checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] + +preinstall_cmd = 'cd %(builddir)s/%(name)s-%(version)s/src && ' +preinstall_cmd += '$CC $CFLAGS -O -c Color_carma.c && ' +preinstall_cmd += '$FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma &&' +preinstall_cmd += 'cp -p carma ../bin/' + +sanity_check_paths = { + 'files': ['bin/carma'], + 'dirs': [''], +} + +tests = ['%(installdir)s/bin/carma'] + +moduleclass = 'lib' From 5b346574f69dd3ef4e9d0237b1cb2b1727a006e3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Dec 2021 22:48:16 +1050 Subject: [PATCH 103/528] dep <- version update --- .../cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb index 02a39c41144..3729e354bab 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb @@ -22,11 +22,11 @@ checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] dependencies = [ ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05', versionsuffix), - ('Biopython', '1.79', versionsuffix), - ('bx-python', '0.8.11', versionsuffix), - ('bcbio-gff', '0.6.7', versionsuffix), - ('scikit-learn', '0.24.2', versionsuffix), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('bcbio-gff', '0.6.7'), + ('scikit-learn', '0.24.2'), ('Pysam', '0.16.0.1'), ] From 930a0c7b5e82daae742a32c6ba5a8828d651a1be Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:33:58 +0000 Subject: [PATCH 104/528] adding easyconfigs: RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb --- .../RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb new file mode 100644 index 00000000000..bcf227398b3 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 784c71c5511687595e4543fdc60c75cdd971c16c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:45:00 +0000 Subject: [PATCH 105/528] adding easyconfigs: ExaML-3.0.22-gompi-2021a-hybrid-avx.eb --- .../ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb new file mode 100644 index 00000000000..9e10f7d38d8 --- /dev/null +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -0,0 +1,35 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ExaML' +version = '3.0.22' +versionsuffix = '-hybrid-avx' + +homepage = 'https://github.com/stamatak/ExaML/' +description = "Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'stamatak' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] + +#prebuildopts = ['cd examl &&', 'cd parser &&'] +#buildopts = ['-f Makefile.OMP.AVX.gcc', '-f Makefile.SSE3.gcc'] +prebuildopts = 'cd examl &&' +buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' + +files_to_copy = [(['examl/examl-OMP-AVX', 'parser/parse-examl'], 'bin'), 'README.md', 'manual'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s examl-OMP-AVX examl"] + +sanity_check_paths = { + 'files': ['bin/examl', 'bin/parse-examl'], + 'dirs': [], +} + +sanity_check_commands = ["examl -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 7d07e5a8b67a0f5fa116bdde78c99541f8638979 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:48:42 +0000 Subject: [PATCH 106/528] adding easyconfigs: TreeMix-1.13-GCC-10.3.0.eb --- .../t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb new file mode 100644 index 00000000000..9baebc6d2dd --- /dev/null +++ b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'TreeMix' +version = '1.13' + +homepage = 'http://bitbucket.org/nygcresearch/treemix' +description = """TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a + set of populations.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://bitbucket.org/nygcresearch/treemix/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fe544f2daa13fd06b20c1a81aac728963ea5b66b75908916ca87ccd7f4cfa3d9'] + +dependencies = [ + ('GSL', '2.7'), + ('Boost', '1.76.0'), +] + +sanity_check_paths = { + 'files': ['bin/treemix'], + 'dirs': [], +} +sanity_check_commands = [("treemix -h | grep 'TreeMix v. %(version)s'", '')] + +moduleclass = 'bio' From d55cf475fdefb8dfc83408e8f028e9f1f8f0b290 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:58:54 +0000 Subject: [PATCH 107/528] Remove commented buildopts --- .../easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb index 9e10f7d38d8..7840f1a156e 100644 --- a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -16,8 +16,6 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] -#prebuildopts = ['cd examl &&', 'cd parser &&'] -#buildopts = ['-f Makefile.OMP.AVX.gcc', '-f Makefile.SSE3.gcc'] prebuildopts = 'cd examl &&' buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' From 33370004c0a5b074d158df88e066264e3b27733e Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Dec 2021 08:31:11 +1050 Subject: [PATCH 108/528] style <- fix redundancy --- .../cDNA_Cupcake-26.0.0-foss-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb new file mode 100644 index 00000000000..9d5bdc5521b --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -0,0 +1,49 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '26.0.0' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('bcbio-gff', '0.6.7'), + ('scikit-learn', '0.24.2'), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = False +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'cupcake'} + +moduleclass = 'bio' From 6d43cd5aacb70b12d0fd258acbca2f37d50c32b9 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Mon, 13 Dec 2021 08:32:39 +1030 Subject: [PATCH 109/528] Delete cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb --- ..._Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 3729e354bab..00000000000 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,50 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v24.2.0 -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'cDNA_Cupcake' -version = '26.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Magdoll/cDNA_Cupcake' -description = """cDNA_Cupcake is a miscellaneous collection of Python and -R scripts used for analyzing sequencing data. -""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('bx-python', '0.8.11'), - ('bcbio-gff', '0.6.7'), - ('scikit-learn', '0.24.2'), - ('Pysam', '0.16.0.1'), -] - -download_dep_fail = False -use_pip = True - -sanity_pip_check = True -sanity_check_paths = { - # check for particular Cupcake ToFU scripts, - # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step - 'files': [ - 'bin/collapse_isoforms_by_sam.py', - 'bin/get_abundance_post_collapse.py', - 'bin/simple_stats_post_collapse.py' - ], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'cupcake'} - -moduleclass = 'bio' From 21f82017b58ebfe9db583e5179b83bb36c4ae350 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Mon, 13 Dec 2021 08:51:39 +1030 Subject: [PATCH 110/528] header <- update --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 9d5bdc5521b..7b6c317aa6a 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -1,6 +1,6 @@ # Contribution by # DeepThought, Flinders University -# Updated to v24.2.0 +# Updated to v26.0.0 # R.QIAO easyblock = 'PythonPackage' From c5f71b97cc80f1921e83054aecf405d86b08814b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 13 Dec 2021 12:10:19 +0100 Subject: [PATCH 111/528] adding easyconfigs: NVHPC-21.11.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb | 75 ++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb new file mode 100644 index 00000000000..201c1d4990e --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb @@ -0,0 +1,75 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.11' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '3b11bcd9cca862fabfce1e7bcaa2050ea12130c7e897f4e7859ba4c155d20720', + local_tarball_tmpl % 'ppc64le': + 'ac51ed92de4eb5e1bdb064ada5bbace5b89ac732ad6c6473778edfb8d29a6527', + local_tarball_tmpl % 'x86_64': + 'd8d8ccd0e558d22bcddd955f2233219c96f7de56aa8e09e7be833e384d32d6aa', + } +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.7/cuda/) +# for NVHPC 21.11, those are: 11.5, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '11.5' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From e416ee8f89e4f5cca11b2de31b05982e903302af Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 13 Dec 2021 12:27:37 +0100 Subject: [PATCH 112/528] adding easyconfigs: ncview-2.1.8-gompi-2021a.eb --- .../n/ncview/ncview-2.1.8-gompi-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb new file mode 100644 index 00000000000..2b6bf793532 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.8' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('UDUNITS', '2.2.28'), + ('X11', '20210518'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From 6564b439610b44727c9d7670e1d57db0a48b6d4f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Dec 2021 21:47:20 +0800 Subject: [PATCH 113/528] adding easyconfigs: EasyBuild-4.5.1.eb --- .../e/EasyBuild/EasyBuild-4.5.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb new file mode 100644 index 00000000000..bc8db12a896 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/b5/ef/8764968b5dc2eedb3eac6ac17e1bc3f7d283b18dd0409d26eefa0f80e720/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/13/16/1b107077b368e713a6cce53fc8b7df4c133ccc19d05818dfdf783d5d7d24/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/2c/77/f529f9e4c07631e4222055e487e26d26cddb4d321c85f64fb08117f73521/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'db6f9013c8cc8501957d23c699cf0eecfffe609a4c0439418325216e11a9be69', # easybuild-framework-4.5.1.tar.gz + '03f10044ddbfe5c48c3257ccd2bbeeecb3b215d0b604efa194ec95d670e7a1d2', # easybuild-easyblocks-4.5.1.tar.gz + 'd1b7e63f733b204a88259dc29fcd10481afd7aacac6ad37b996841ddd733f72b', # easybuild-easyconfigs-4.5.1.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From dfbf7947ddbcd95ef54e6417cf45db3e78149397 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Dec 2021 18:40:12 +0000 Subject: [PATCH 114/528] add yaml-cpp to Trilinos --- ...rilinos-12.12.1-foss-2019b-Python-3.7.4.eb | 1 + .../yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb index bcf9ccb2baf..c4ee42f5588 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb @@ -50,6 +50,7 @@ dependencies = [ ('MATIO', '1.5.17'), ('GLM', '0.9.9.8'), ('X11', '20190717'), + ('yaml-cpp', '0.6.3'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..083cd98d36b --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.6.3' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['77ea1b90b3718aa0c324207cb29418f5bced2354c2e483a9523d98c3460af1ed'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' From 9584bb4f0b554aebe615a0acc93fa1017c9f77b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Dec 2021 15:18:40 +0100 Subject: [PATCH 115/528] bump version to 4.5.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0a073c359c8..bb5b73a292d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.1' +VERSION = '4.5.2.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From d9202198d587f65f098177e6724e8f63a8a9b760 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 13 Dec 2021 19:50:45 +0000 Subject: [PATCH 116/528] adding easyconfigs: elbencho-2.0-3-GCC-10.3.0.eb --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb new file mode 100644 index 00000000000..12d37d0e06b --- /dev/null +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = "MakeCp" + +name = "elbencho" +version = "2.0-3" + +homepage = "https://github.com/breuner/elbencho" +description = """ A distributed storage benchmark for files, objects & blocks with support for GPUs""" + + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +dependencies = [('Boost', '1.76.0'), ('libaio', '0.3.112')] + +sources = [{ + 'filename': "v%(version)s.tar.gz", + 'git_config': { + 'url': 'https://github.com/breuner', + 'repo_name': 'elbencho', + 'tag': 'v%(version)s' + }, + +}] +checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] + +files_to_copy = ["bin"] +sanity_check_paths = { + 'dirs': files_to_copy, + 'files': ['bin/%s' % x for x in + ['elbencho', 'elbencho-unstripped']], +} From 5652c4366eb1583daa923a727d95bc229ed63d63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 13 Dec 2021 22:14:23 +0100 Subject: [PATCH 117/528] adding easyconfigs: MicrobeAnnotator-2.0.5-foss-2021a.eb --- .../MicrobeAnnotator-2.0.5-foss-2021a.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb new file mode 100644 index 00000000000..1635e196613 --- /dev/null +++ b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'MicrobeAnnotator' +version = '2.0.5' + +homepage = 'https://github.com/cruizperez/MicrobeAnnotator' +description = "Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.11'), + ('HMMER2', '2.3.2'), + ('python-isal', '0.11.0'), + ('SciPy-bundle', '2021.05'), + ('Seaborn', '0.11.2'), + ('wget', '1.21.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('attrs', '21.2.0', { + 'modulename': 'attr', + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], + }), + ('psutil', '5.8.0', { + 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], + }), + ('wget', '3.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], + }), + ('importlib_resources', '5.4.0', { + 'checksums': ['d756e2f85dd4de2ba89be0b21dba2a3bbec2e871a42a3a16719258a11f87506b'], + }), + ('xopen', '1.2.1', { + 'checksums': ['9cb1e23592b1ee0f7b067a67f74fcc7957e08821cb2a0e1f6b6c87499c68afcf'], + }), + ('fasta-reader', '1.0.0', { + 'checksums': ['61453b968a71ddf5bb63172f68d73ba2ccf0a23ac3b6ae0f6c63afa478d30444'], + }), + ('gff-io', '0.0.2', { + 'checksums': ['b1691222494787995a14b4b9ca5cbd3ead1372c4f6e5b58ef71ed733a35d7a59'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('hmmer', '0.1.0', { + 'checksums': ['4d322ae026c0a61459cef06405add39ea86f7ad1fef845712b7b27b4e6842a92'], + }), + (name, version, { + 'preinstallopts': 'sed -i "/python_requires/d" setup.py && ', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/cruizperez/MicrobeAnnotator/archive/'], + 'checksums': ['4bc128faf725164b50c20026530425336d72fbfd6916f8f8c6c8c5246c7b43ad'], + }), +] + +sanity_check_commands = [ + 'microbeannotator -h', + 'microbeannotator_db_builder -h', +] + +moduleclass = 'bio' From 3452676b333f4dbfcf211c9d335e7d5c51844a60 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:40:33 +0000 Subject: [PATCH 118/528] adding easyconfigs: Bowtie2-2.4.4-GCC-11.2.0.eb --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..24d2f6861d9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.4' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + +moduleclass = 'bio' From b0022b94ca56c0b48926f27727f0f316c8827587 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:41:31 +0000 Subject: [PATCH 119/528] adding easyconfigs: Bismark-0.23.1-foss-2021b.eb --- .../b/Bismark/Bismark-0.23.1-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb new file mode 100644 index 00000000000..af597f02e72 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.23.1' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2ceb620cfc3f1c869f4bda656ab01c242f1da7ec01615b0d23b28c702147a337'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Bowtie2', '2.4.4'), + ('SAMtools', '1.14'), +] + +sanity_check_commands = [ 'bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 6ee6b9e50e8a3537a2519f5a61630236096c406f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:46:59 +0000 Subject: [PATCH 120/528] adding easyconfigs: ISA-L-2.30.0-GCCcore-11.2.0.eb --- .../i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..319c7856561 --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' From c88adfbd28a098ee77efe1521710d306854381d7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:49:16 +0000 Subject: [PATCH 121/528] adding easyconfigs: libdeflate-1.8-GCCcore-11.2.0.eb --- .../libdeflate-1.8-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..da97e2fb5c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.8' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['50711ad4e9d3862f8dfb11b97eb53631a86ee3ce49c0e68ec2b6d059a9662f61'] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From 0e343b1279fcd604a0132b237bd802a7316094b4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:50:47 +0000 Subject: [PATCH 122/528] adding easyconfigs: fastp-0.23.2-GCC-11.2.0.eb --- .../f/fastp/fastp-0.23.2-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..3811081f326 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.2' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libdeflate', '1.8'), + ('ISA-L', '2.30.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From d0ed63f325049fef9bdb8f97ebefbecdc2333c07 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 23:00:41 +0000 Subject: [PATCH 123/528] adding easyconfigs: MAGMA-1.09b-GCC-11.2.0.eb --- .../m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb new file mode 100644 index 00000000000..eb16168b20f --- /dev/null +++ b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'MAGMA' +version = '1.09b' + +homepage = 'https://ctg.cncr.nl/software/magma' +description = """MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. +It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous +GWAS or meta-analysis.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + 'https://ctg.cncr.nl/software/MAGMA/prog/', + 'https://ctg.cncr.nl/software/MAGMA/prog/archive/', +] +sources = ['%(namelower)s_v%(version)s_source.zip'] +checksums = ['8af8673fa6c3cf60c2528a06783c20795d9daf4649481cd6e04feb68b91730e0'] + +buildopts = ' CXX=${CXX}' + +files_to_copy = [ + (['magma'], 'bin'), + (['manual_v%(version)s.pdf'], 'doc'), + 'CHANGELOG', + 'COPYRIGHT', +] + +sanity_check_commands = ['magma --version'] + +sanity_check_paths = { + 'files': ['bin/magma'], + 'dirs': [], +} + +moduleclass = 'bio' From 3ca3588f715ad52fceb429b80bbf3789e787675d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 14 Dec 2021 00:26:51 +0100 Subject: [PATCH 124/528] adding easyconfigs: OpenFace-2.2.0-foss-2021a.eb, dlib-19.22-foss-2021a.eb, OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb, dlib-19.22-foss-2021a-CUDA-11.3.1.eb --- .../dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++ .../d/dlib/dlib-19.22-foss-2021a.eb | 31 +++++++++++ .../OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 53 +++++++++++++++++++ .../o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 50 +++++++++++++++++ 4 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..95635f71e04 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'dlib' +version = '19.22' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +toolchain = {'name': 'foss', 'version': '2021a'} # requires blas +toolchainopts = {'pic': True} + +github_account = 'davisking' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), +] + +sanity_check_paths = { + 'files': ['include/dlib/image_io.h', 'lib/libdlib.a', 'lib64/libdlib.a'], + 'dirs': ['lib/pkgconfig', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb new file mode 100644 index 00000000000..b3c3383dcf6 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'dlib' +version = '19.22' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'davisking' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['include/dlib/image_io.h', 'lib/libdlib.a', 'lib64/libdlib.a'], + 'dirs': ['lib/pkgconfig', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ed5e27cab78 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'OpenFace' +version = '2.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/TadasBaltrusaitis/OpenFace' +description = """OpenFace – a state-of-the art tool intended for facial landmark +detection, head pose estimation, facial action unit recognition, and eye-gaze +estimation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'TadasBaltrusaitis' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +checksums = [ + '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz + '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('patchelf', '0.12') +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), + ('dlib', '19.22', '-CUDA-%(cudaver)s'), + ('SDL2', '2.0.14'), + ('Boost', '1.76.0'), +] + +configopts = "-DCMAKE_BUILD_TYPE=RELEASE" + +# This is the only way I found to remove the banned OpenBLAS from libraries +# required by the OpenFace executables, as CMake stubbornly includes it there +preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' +preinstallopts += ' bin/FaceLandmarkVidMulti bin/FaceLandmarkImg bin/FeatureExtraction && ' + +sanity_check_paths = { + 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], + 'dirs': [], +} +sanity_check_commands = [ + 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb new file mode 100644 index 00000000000..3279d8b139f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'OpenFace' +version = '2.2.0' + +homepage = 'https://github.com/TadasBaltrusaitis/OpenFace' +description = """OpenFace – a state-of-the art tool intended for facial landmark +detection, head pose estimation, facial action unit recognition, and eye-gaze +estimation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'TadasBaltrusaitis' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +checksums = [ + '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz + '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('patchelf', '0.12') +] +dependencies = [ + ('OpenCV', '4.5.3', '-contrib'), + ('dlib', '19.22'), + ('SDL2', '2.0.14'), + ('Boost', '1.76.0'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +# This is the only way I found to remove the banned OpenBLAS from libraries +# required by the OpenFace executables, as CMake stubbornly includes it there +preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' +preinstallopts += ' bin/FaceLandmarkVidMulti bin/FaceLandmarkImg bin/FeatureExtraction && ' + +sanity_check_paths = { + 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], + 'dirs': [], +} +sanity_check_commands = [ + 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' +] + +moduleclass = 'lib' From 2c4ab81fe58b509dad3c8142fb2ae15ad7bf6de9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 14 Dec 2021 13:48:22 +0000 Subject: [PATCH 125/528] adding easyconfigs: ShengBTE-1.1.1-foss-2021a.eb --- .../s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb new file mode 100644 index 00000000000..de135d9fb64 --- /dev/null +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ShengBTE' +version = '1.1.1' + +homepage = 'https://bitbucket.org/sousaw/shengbte' +description = "A solver for the Boltzmann transport equation for phonons." + +toolchain = {'name': 'foss', 'version': '2021a'} + +bitbucket_account = 'sousaw' +source_urls = [BITBUCKET_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['617a7110f4222ee249e351d15805d74744a550f01c07d798615d697de26edd71'] + +dependencies = [('spglib', '1.16.2')] + +start_dir = 'Src' + +# strip "include arch.make" -- not needed as we already set necessary env vars +prebuildopts = "sed -i '1d' Makefile && " +# -fallow-argument-mismatch needed for GCC 10+ +buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' + +files_to_copy = [([name], 'bin'), 'Test-*', 'LICENSE', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [ + "cd %%(builddir)s/*%%(namelower)s*/Test-%s && mpirun -n %%(parallel)s %%(name)s" % x for x in ['QE', 'RTA', 'VASP'] +] + +moduleclass = 'phys' From ac26de38dad3ad47862dac4a722fff6f66576b95 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 01:09:27 +1050 Subject: [PATCH 126/528] dep <- sklearn path --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 7b6c317aa6a..e2904528e42 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -29,9 +29,11 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = False +download_dep_fail = True use_pip = True +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, From 04a5f90257e31582e80064946d576a6109486981 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 00:52:09 +1030 Subject: [PATCH 127/528] Update easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb Co-authored-by: Sam Moors --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index d9470e12178..bf0b8def215 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -30,9 +30,11 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = False +download_dep_fail = True use_pip = True +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, From 1d7c443b6ae88e7817287375bbd14ef18d520746 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Dec 2021 17:32:18 +0100 Subject: [PATCH 128/528] strip out non-required binutils/CMake build dependencies + attrs/psutil extensions from MicrobeAnnotator easyconfig --- .../MicrobeAnnotator-2.0.5-foss-2021a.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb index 1635e196613..b76e1fa7bff 100644 --- a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb @@ -8,11 +8,6 @@ description = "Easy-to-use pipeline for the comprehensive metabolic annotation o toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), @@ -29,13 +24,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('attrs', '21.2.0', { - 'modulename': 'attr', - 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], - }), - ('psutil', '5.8.0', { - 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], - }), ('wget', '3.2', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], From 51c455fa10976769c71f292c3e930dd409839380 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 19:08:56 +0100 Subject: [PATCH 129/528] adding easyconfigs: CHERAB-1.3.0-intel-2020b.eb, Raysect-0.7.1-intel-2020b.eb --- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 30 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 24 +++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb new file mode 100644 index 00000000000..a1ad1f6bc92 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = False + +sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb new file mode 100644 index 00000000000..d506edd8c8c --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +moduleclass = 'vis' From b41ebf27904c54cd360bac8b4581587e28f9d23f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 20:52:03 +0100 Subject: [PATCH 130/528] adding easyconfigs: STRUMPACK-6.1.0-foss-2020b.eb, STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 52 ++++++++++++++++++ .../STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 53 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb new file mode 100644 index 00000000000..26e9142f8f1 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb new file mode 100644 index 00000000000..4938fb4262b --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' From 56fb50c80846199255be0b8ec23d07f5a2e2eb73 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 21:02:20 +0100 Subject: [PATCH 131/528] CHERAB/1.3.0 style corrections --- easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index a1ad1f6bc92..7d3d731a92e 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -10,7 +10,6 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] @@ -25,6 +24,9 @@ download_dep_fail = True use_pip = True sanity_pip_check = False -sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] +sanity_check_commands = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' + 'python -c "import cherab"' +] moduleclass = 'phys' From 981670054d1d3e0b22bd4a6e032a4cece2b1c419 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Dec 2021 08:59:37 +0000 Subject: [PATCH 132/528] update source location --- .../Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb index c4ee42f5588..e5f08d8c161 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb @@ -10,11 +10,8 @@ description = """The Trilinos Project is an effort to develop algorithms and ena toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True, 'strict': True} -source_urls = [ - 'http://trilinos.csbsju.edu/download/files/', - 'https://trilinos.org/oldsite/download/files/', -] -sources = ['%(namelower)s-%(version)s-Source.tar.gz'] +source_urls = ['https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/trilinos/12.12.1-5/'] +sources = ['%(namelower)s_%(version)s.orig.tar.bz2'] patches = [ ('Trilinos-%(version)s_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'), 'Trilinos-%(version)s_fix-Py3.patch', @@ -23,7 +20,7 @@ patches = [ 'Trilinos-%(version)s_py3_fixes_and_more.patch', ] checksums = [ - '7c67d83befbeabc773661bcdfee2850c404d249160b755d3f1be2e96f564f9fd', # trilinos-12.12.1-Source.tar.gz + '5d0d84cb794f94927dd4785efe89eacc823b659dbe9f8273ab86e86ed4396db7', # trilinos_12.12.1.orig.tar.bz2 'de2e989bf9e7cbe7cab9126a464b5b1569983de4060956e7a95dccb9e0bad039', # Trilinos-12.12.1_fix-CEpetra-LAPACK.patch '5505645b712056403263860de86efccfb343cb5e5bf8d65697526d65ea5df099', # Trilinos-12.12.1_fix-Py3.patch # Trilinos-12.12.1_muelu-fix-function-signature.patch From 9708169c6a13a364d4cd1d45b9e3976a0a597287 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:14:57 +1050 Subject: [PATCH 133/528] adding easyconfigs: PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb --- .../PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d033ab417bb --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['26d150d37159406f678165bf3d6cb06b3021fb2227b301b06095e769c87bdd9f'] + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('DendroPy', '4.4.0'), + ('matplotlib', '3.2.1', versionsuffix), + ('Seaborn', '0.10.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From ee9e93ec0f7195da189dd767b1ae3cbc1f01b97d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:20:51 +1050 Subject: [PATCH 134/528] dep <- phylophlan + --- .../MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d2b2b7fdc2b..a6979c9e19d 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -1,12 +1,6 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# Software License:: MIT -# -# Notes:: -## +# Contribution by +# DeepThought, Flinders University +# R.QIAO easyblock = 'PythonPackage' @@ -33,10 +27,11 @@ dependencies = [ ('CMSeq', '1.0.3', versionsuffix), ('biom-format', '2.1.10', versionsuffix), ('h5py', '2.10.0', versionsuffix), + ('PhyloPhlAn', '3.0', versionsuffix), ] use_pip = True -download_dep_fail = False +download_dep_fail = True sanity_pip_check = True sanity_check_paths = { From fd932e91c9bd80f48d5d9facdf16c5edebac0e77 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:17:26 +1030 Subject: [PATCH 135/528] sanity_check_commands + --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index bf0b8def215..2843b05ef3c 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -47,6 +47,12 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'collapse_isoforms_by_sam.py', + 'get_abundance_post_collapse.py', + 'simple_stats_post_collapse.py', +] + options = {'modulename': 'cupcake'} moduleclass = 'bio' From 875c909dc704c32aaf7a2693b5a99a4efed6e910 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:18:29 +1030 Subject: [PATCH 136/528] sanity_check_commands + --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index e2904528e42..99bc2687837 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -46,6 +46,12 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'collapse_isoforms_by_sam.py', + 'get_abundance_post_collapse.py', + 'simple_stats_post_collapse.py', +] + options = {'modulename': 'cupcake'} moduleclass = 'bio' From 021efa6d7929d7e6aa942fd0b3fbbbf41dc74f7f Mon Sep 17 00:00:00 2001 From: Mustafa Abduljabbar Date: Wed, 15 Dec 2021 11:57:34 +0100 Subject: [PATCH 137/528] Update easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb index ba0edb4190a..a59fbf59592 100644 --- a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb @@ -1,4 +1,4 @@ -easyblock='PackedBinary' +easyblock = 'PackedBinary' name = 'Schrodinger' version = '2021-4' From 9aa7a0c8ba4daedc84026a672025d52ac45801d2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:55:21 +1050 Subject: [PATCH 138/528] adding easyconfigs: PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb --- ...hyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..02454b8e66d --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 3c5f93660e47c39bd9ac9df51a9e897cdc74fbc7 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:57:28 +1050 Subject: [PATCH 139/528] checksum + --- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb index 02454b8e66d..964b716cb7b 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb @@ -19,6 +19,7 @@ at multiple levels of resolution. source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] toolchain = {'name': 'foss', 'version': '2021a'} From d3ddd0891363593d49785ae9350a626c50354f61 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 22:16:08 +1050 Subject: [PATCH 140/528] style <- versionsuffix drop --- .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb new file mode 100644 index 00000000000..7cdf357fcbf --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From a307cb63188920aa194940e9f926b3563212985d Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:56:25 +1030 Subject: [PATCH 141/528] Delete PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb --- ...hyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 964b716cb7b..00000000000 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v3.0.2 - -easyblock = 'PythonPackage' - -name = 'PhyloPhlAn' -version = '3.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/biobakery/phylophlan' -description = """ -PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of -genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method -for large-scale microbial genome characterization and phylogenetic analysis -at multiple levels of resolution. -""" - -source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('DendroPy', '4.5.2'), - ('matplotlib', '3.4.2'), - ('Seaborn', '0.11.2'), -] - -use_pip = True -download_dep_fail = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], - 'dirs': ['lib'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -options = {'modulename': '%(namelower)s'} - -moduleclass = 'bio' From fe10dadcb3698a78fd9e52236b435c49a7c4d9c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 15 Dec 2021 12:54:43 +0100 Subject: [PATCH 142/528] OpenFace: add missing patchfile --- .../OpenFace-2.2.0-use_FlexiBLAS.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch new file mode 100644 index 00000000000..105de6d5362 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch @@ -0,0 +1,31 @@ +diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt +--- ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt 2019-07-13 20:20:17.000000000 +0200 ++++ ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt 2021-12-13 23:43:45.160326152 +0100 +@@ -11,22 +11,19 @@ + set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_CONFIG_DIR}") + add_definitions(-DCONFIG_DIR="${CONFIG_DIR}") + +-# make sure we'll use OpenBLAS only: there's a header file naming difference between different +-# implementations; so OpenFace wants OpenBLAS; +-find_package(OpenBLAS REQUIRED) +-if ( ${OpenBLAS_FOUND} ) ++if ( DEFINED ENV{LIBBLAS} ) ++ SET(OpenBLAS_LIB "-L$ENV{BLAS_LIB_DIR} $ENV{LIBBLAS}") + MESSAGE("OpenBLAS information:") + MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") + else() + MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") + endif() + +-if ( ${OpenBLAS_INCLUDE_FOUND} ) ++if ( DEFINED ENV{BLAS_INC_DIR} ) ++ SET(OpenBLAS_INCLUDE_DIR $ENV{BLAS_INC_DIR}) + MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") + else() +- MESSAGE(WARNING "OpenBLAS include not found in the system. Using the one vended with OpenFace.") +- set(OpenBLAS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/lib/3rdParty/OpenBLAS/include") +- MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") ++ MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") + endif() + + find_package( OpenCV 4.0 REQUIRED COMPONENTS core imgproc calib3d highgui objdetect) From 042a094a185038f0766fd0360487df1f02f3689c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 13:49:23 +0100 Subject: [PATCH 143/528] use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) --- .../w/worker/worker-1.6.12-foss-2019a.eb | 67 +++---------------- 1 file changed, 11 insertions(+), 56 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb index af9f61a3831..96c86b0cd39 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb @@ -8,80 +8,35 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = SYSTEM +local_tcname = 'foss' +local_tcver = '2019a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['503ad9db78d949999bd5f3ba15b18f746cad2eaf2ff49240398b2b6792f9ffbd'] -osdependencies = ['perl'] - -local_tcname = 'foss' -local_tcver = '2019a' -builddependencies = [(local_tcname, local_tcver)] -versionsuffix = '-%s-%s' % (local_tcname, local_tcver) - -exts_defaultclass = 'PerlModule' - -exts_list = [ - ('Config::General', '2.63', { - 'source_tmpl': 'Config-General-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], - 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], - }), - ('IO::Stringy', '2.113', { - 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/'], - 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], - }), - ('Text::CSV', '2.00', { - 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], - }), - ('DBI', '1.643', { - 'source_tmpl': 'DBI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], - 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], - }), - ('DBD::SQLite', '1.64', { - 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], - }), - ('Date::Language', '2.32', { - 'source_tmpl': 'TimeDate-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC/'], - 'checksums': ['34eca099e375e2d142ea6cc935922c4980dc21c65ce7c24823ca08457c4bb3d6'], - }), - ('Template', '3.008', { - 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['52400f68bef6731b0fca00e3438ed835b29ab9fec72a404866dee8fc139da692'], - }), +dependencies = [ + ('Perl', '5.28.1') ] -preconfigopts = "export CC=mpicc && " - -modextrapaths = { - 'PERL5LIB': ['share/perl5', 'lib64/perl5'], -} - # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % local_tcname, 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['dbilogstrip', 'dbiprof', 'dbiproxy', 'tpage', 'ttree', 'wcat', 'wconvert', - 'wload', 'worker', 'wreduce', 'wresume', 'wsub', 'wsummarize']], - 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], } sanity_check_commands = ["wsub -help"] From 6f5eeaafb1633ce16dd586edd4e583e00986a3a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 15 Dec 2021 13:56:46 +0100 Subject: [PATCH 144/528] OpenFace: use a working sanity check command --- .../o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 4 +--- easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index ed5e27cab78..ffd3307a288 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -46,8 +46,6 @@ sanity_check_paths = { 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], 'dirs': [], } -sanity_check_commands = [ - 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' -] +sanity_check_commands = ['FeatureExtraction | grep OpenFace'] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb index 3279d8b139f..9f269dc9eb2 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -43,8 +43,6 @@ sanity_check_paths = { 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], 'dirs': [], } -sanity_check_commands = [ - 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' -] +sanity_check_commands = ['FeatureExtraction | grep OpenFace'] moduleclass = 'lib' From 3ba6730c27fb628dee16565cc84a3b4a87c24ae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 14:19:24 +0100 Subject: [PATCH 145/528] adding easyconfigs: worker-1.6.12-foss-2021b.eb --- .../w/worker/worker-1.6.12-foss-2021b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb new file mode 100644 index 00000000000..9657cb67905 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.12' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'foss' +local_tcver = '2021b' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['503ad9db78d949999bd5f3ba15b18f746cad2eaf2ff49240398b2b6792f9ffbd'] + +dependencies = [ + ('Perl', '5.34.0') +] + +# need to replace MPI_Type_struct by MPI_Type_create_struct, since MPI_Type_struct was removed in MPI 3.0; +# see also https://github.com/gjbex/worker/pull/45 +preconfigopts = "sed -i 's/MPI_Type_struct/MPI_Type_create_struct/g' src/worker.c && " + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 32/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % local_tcname, + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 49626287a830b24989daa75f6c13d42e98095f8f Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:24:53 +1030 Subject: [PATCH 146/528] Update easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb Co-authored-by: Sam Moors --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 2843b05ef3c..b04f48e2a2d 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -48,9 +48,9 @@ sanity_check_paths = { } sanity_check_commands = [ - 'collapse_isoforms_by_sam.py', - 'get_abundance_post_collapse.py', - 'simple_stats_post_collapse.py', + 'collapse_isoforms_by_sam.py -h', + 'get_abundance_post_collapse.py -h', + 'simple_stats_post_collapse.py -h', ] options = {'modulename': 'cupcake'} From e08fca9f8178cd75e0a3a31e67193ebc0c381bfd Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 15 Dec 2021 13:55:47 +0000 Subject: [PATCH 147/528] added moduleclass --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 12d37d0e06b..4b5db8af46f 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -28,3 +28,5 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], } + +moduleclass = 'tools' From 9d6a99c05dc4470e4bac624d629ebf20ea26826e Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:26:16 +1030 Subject: [PATCH 148/528] debug <- sanity_check --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 99bc2687837..e9c3fd9ba0c 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -39,9 +39,9 @@ sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step 'files': [ - 'bin/collapse_isoforms_by_sam.py', - 'bin/get_abundance_post_collapse.py', - 'bin/simple_stats_post_collapse.py' + 'bin/collapse_isoforms_by_sam.py -h', + 'bin/get_abundance_post_collapse.py -h', + 'bin/simple_stats_post_collapse.py -h' ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From f1c916d3c8f23f115e75faf587fc894a2c8adec7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 14:57:38 +0100 Subject: [PATCH 149/528] Update style of Raysect v0.7.1 EB files --- .../r/Raysect/Raysect-0.7.1-foss-2020b.eb | 25 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 3 ++- 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb new file mode 100644 index 00000000000..53e51415d54 --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb index d506edd8c8c..0d104c5782b 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -9,7 +9,6 @@ description = """Raysect is an OOP ray-tracing framework for Python""" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] @@ -20,5 +19,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True +sanity_pip_check = True moduleclass = 'vis' From c15e2c01775ec14bd2e7c7a73cd3b3908f7254b9 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:28:22 +1030 Subject: [PATCH 150/528] Update cDNA_Cupcake-26.0.0-foss-2021a.eb --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index e9c3fd9ba0c..f088e26620f 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -39,17 +39,17 @@ sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step 'files': [ - 'bin/collapse_isoforms_by_sam.py -h', - 'bin/get_abundance_post_collapse.py -h', - 'bin/simple_stats_post_collapse.py -h' + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ - 'collapse_isoforms_by_sam.py', - 'get_abundance_post_collapse.py', - 'simple_stats_post_collapse.py', + 'collapse_isoforms_by_sam.py -h', + 'get_abundance_post_collapse.py -h', + 'simple_stats_post_collapse.py -h', ] options = {'modulename': 'cupcake'} From 0917f4ae0bdbfc12e01cd1bd7e96e836b8f4e38c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 15:05:43 +0100 Subject: [PATCH 151/528] ParMETIS v4.0.3 for iimpi/2020b --- .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb new file mode 100644 index 00000000000..8cc997b5624 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From b4acc3452ea84c11d76645410c3e053f3725ac1e Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 15 Dec 2021 15:55:48 +0100 Subject: [PATCH 152/528] adding easyconfigs: phonopy-2.12.0-foss-2020b.eb --- .../p/phonopy/phonopy-2.12.0-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb new file mode 100644 index 00000000000..3a1f3d0bc3b --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.12.0' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ff65065f418ccbff9fbc1186b9a65581e83b42789aa4a656f45badfff9bd3f61'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('h5py', '3.1.0'), + ('spglib-python', '1.16.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From 58273fa594087e103e5184c7ca16772bfa1868f1 Mon Sep 17 00:00:00 2001 From: smoretti Date: Wed, 15 Dec 2021 15:28:17 +0100 Subject: [PATCH 153/528] Add an exception in the test suite for multiple Rgurobi versions in the same toolchain --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bb0cdb9507a..55604601ca5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -331,8 +331,8 @@ def check_dep_vars(self, gen, dep, dep_vars): dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]: + # same goes for WRF and WPS; Gurobi and Rgurobi + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: if dep == dep_name and len(dep_vars) > 1: for key in list(dep_vars): ecs = dep_vars[key] From 0c28cfb57d9f25f537d9bd59e70eded8b4033742 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Dec 2021 16:16:29 +0100 Subject: [PATCH 154/528] adding easyconfigs: MATLAB-2021b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb new file mode 100644 index 00000000000..1f98eb7c6df --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb @@ -0,0 +1,27 @@ +name = 'MATLAB' +version = '2021b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%(version)s_Linux.iso'] +checksums = ['d8e75bda06b45edf2c68cda6761fac077b7bfa7b7779db0c95e098b5c695f4cc'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server = 'my-license-server' +# license_server_port = '1234' + +moduleclass = 'math' From 04358083e7ad2b66aff2bd7bc4604291127ddb20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 16:16:37 +0100 Subject: [PATCH 155/528] adding easyconfigs: dill-0.3.4-GCCcore-11.2.0.eb --- .../d/dill/dill-0.3.4-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d6147e812d7 --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.4' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_ZIP] +checksums = ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From ac5f9a7a6902d21fec40aea7d79bdec28dcf9eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:00:56 +0100 Subject: [PATCH 156/528] {*}[foss/2021b] leidenalg v0.8.8, python-igraph v0.9.8, arpack-ng v3.8.0, PyCairo v1.20.1 (+ deps) w/ Python 3.9.6 --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb | 35 ++++++++++++ .../e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb | 21 ++++++++ .../i/igraph/igraph-0.9.5-foss-2021b.eb | 51 ++++++++++++++++++ .../l/leidenalg/leidenalg-0.8.8-foss-2021b.eb | 53 +++++++++++++++++++ .../PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb | 44 +++++++++++++++ .../python-igraph-0.9.8-foss-2021b.eb | 53 +++++++++++++++++++ 6 files changed, 257 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb new file mode 100644 index 00000000000..ba40c98ecc2 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.8.0' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..29a8b27adc6 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.37'), # to make CMake compiler health check pass on old systems + ('CMake', '3.21.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb new file mode 100644 index 00000000000..004d9503d9c --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.9.5' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['c4e3f67892e1e287865d799162406b3f94916ad6f2cc069a9239e36ca495a17a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('arpack-ng', '3.8.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +_includes = ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']] +_libs = ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _includes + _libs, + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb new file mode 100644 index 00000000000..ee2a8af4bb9 --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.8' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('PyYAML', '5.4.1'), + ('Bison', '3.7.6'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('igraph', '0.9.5'), + ('python-igraph', '0.9.8'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = "python setup.py build --use-pkg-config && " +# 'python-igraph' dependency was renamed to 'igraph' +local_preinstallopts += "sed -i 's/python-igraph >=/igraph >=/g' setup.py && " + +exts_list = [ + ('ddt', '1.4.4', { + 'checksums': ['8de39a69730442dc835e4d33f9d2e33043ff91151c8d18086959ee556febb9f8'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['12750f66d1f0c84ed4484fa895a9d5a163e2f4b611edb12ad09cc66120654df3'], + }), +] + +sanity_check_commands = [ + # tests require that 'leidenalg' Python module is available, + # so needs to be run after installation + "cd %(builddir)s/leidenalg/leidenalg-%(version)s && python setup.py test --use-pkg-config", + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d1fb5b548db --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.20.1' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee72b035b21a475e1ed648e26541b04e5d7e753d75ca79de8c583b25785531b'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb new file mode 100644 index 00000000000..f16f7fbcc66 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.9.8' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('igraph', '0.9.5'), + ('PyCairo', '1.20.1'), + ('Clang', '12.0.1'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.4', { + 'checksums': ['42ee7b9e15f7b225747c3fa08f43c5d6c83bc899f80ff9bae9319334824076e9'], + }), + ('igraph', version, { + 'installopts': '--install-option="--use-pkg-config"', + 'modulename': 'igraph', + 'patches': ['python-igraph-0.9.0_fix-igraph-libs.patch'], + 'checksums': [ + 'e7bad9f5f52e6dc3ccdaa3d02d8ec433d9ada704f7a83168915cfa0c4c226730', # igraph-0.9.8.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +sanity_pip_check = True + +moduleclass = 'lib' From 5311bcf4ce3ab47d652817b1815ba18986d6665c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:10:02 +0100 Subject: [PATCH 157/528] add custom sanity check command for Rgurobi --- .../easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb | 2 ++ .../easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb index db19965911d..49cccf32791 100644 --- a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['gurobi'], } +sanity_check_commands = ["echo 'library(gurobi)' | R -q --no-save"] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb index c66061a04a9..d21fd11e0be 100644 --- a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['gurobi'], } +sanity_check_commands = ["echo 'library(gurobi)' | R -q --no-save"] + moduleclass = 'math' From a4ba6c87daea2d9f17d2524d171fbc34cc3f25b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:13:21 +0100 Subject: [PATCH 158/528] adding easyconfigs: h5py-3.6.0-foss-2021b.eb, h5py-3.6.0-intel-2021b.eb --- .../h/h5py/h5py-3.6.0-foss-2021b.eb | 34 +++++++++++++++++++ .../h/h5py/h5py-3.6.0-intel-2021b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb new file mode 100644 index 00000000000..0240e4f1dd4 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.6.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['8752d2814a92aba4e2b2a5922d2782d0029102d99caaf3c201a566bc0b40db29'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb new file mode 100644 index 00000000000..067d8089229 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.6.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['8752d2814a92aba4e2b2a5922d2782d0029102d99caaf3c201a566bc0b40db29'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' From 4c50e66f57759373316d546d6aaf25b21e505d53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:17:24 +0100 Subject: [PATCH 159/528] adding easyconfigs: statsmodels-0.13.1-foss-2021b.eb, statsmodels-0.13.1-intel-2021b.eb --- .../statsmodels-0.13.1-foss-2021b.eb | 29 +++++++++++++++++++ .../statsmodels-0.13.1-intel-2021b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb new file mode 100644 index 00000000000..1ff812f4807 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb new file mode 100644 index 00000000000..3ccebf046b6 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' From 2a668e70a2347d4f621d811f4814b8f11bf86646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:54:15 +0100 Subject: [PATCH 160/528] adding easyconfigs: scanpy-1.8.2-foss-2021b.eb --- .../s/scanpy/scanpy-1.8.2-foss-2021b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb new file mode 100644 index 00000000000..278254f6aa8 --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.8.2' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('networkx', '2.6.3'), + ('numba', '0.54.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.62.3'), + ('leidenalg', '0.8.8'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.0.2', { + 'checksums': ['feb87e0ce1dc1f8f3f21e18a85216c790e746d76a5ff6889563394605f504a2b'], + }), + # anndata 0.7.8 needs xlrd<2.0 + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('anndata', '0.7.8', { + 'checksums': ['1efd7eb40839e0325bb066238280228a980d7dde6410793dbff2835f44a2d3ef'], + }), + ('pynndescent', '0.5.5', { + 'checksums': ['7a7df8412b19cfb3596060faf5a8c5d0bf5b3bd504f8efd900fc4e3918c6f882'], + }), + ('umap-learn', '0.5.2', { + 'modulename': 'umap', + 'checksums': ['0ede8921c3ef0e1976cdc91b533b2bce82471c87dbb9fad447f617ca5b881d52'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + (name, version, { + 'checksums': ['0c0baa6f08cec50b89b512cef3bfc7f612b215ce02c0fb49cc01c2acfbb2e9bb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From 193a9efdbbebc42eebf7015a9cdb2dd38bbf8100 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Dec 2021 17:02:15 +0000 Subject: [PATCH 161/528] adding easyconfigs: annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb --- ...var-20191024-GCCcore-11.2.0-Perl-5.34.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb new file mode 100644 index 00000000000..91bdfccb8ef --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb @@ -0,0 +1,42 @@ +# Toolchain updated to GCCcore-11.2 +# Downloaded tarball has same checksum as the one from 20191024 +# J. Sassmannshausen /NHS/GSTT + +easyblock = 'Tarball' + +name = 'annovar' +# Unconventional version is taken from the upstream site +# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ +version = '20191024' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human +genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# Registration required for download +# http://download.openbioinformatics.org/annovar_download_form.php +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] + +dependencies = [('Perl', '5.34.0')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +sanity_check_commands = [ + 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', +] + +moduleclass = 'bio' From 3b9d67b3cfce7cbe5521488a21cde43f4686d220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 18:02:51 +0100 Subject: [PATCH 162/528] include output of failing code style check in message produced by failing easyconfigs style test --- test/easyconfigs/styletests.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index ec27d234b46..91f39820898 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -29,9 +29,10 @@ """ import glob -from unittest import TestCase, TestLoader, main, skipIf +from unittest import TestLoader, main, skipIf from easybuild.base import fancylogger +from easybuild.base.testing import TestCase from easybuild.framework.easyconfig.tools import get_paths_for from easybuild.framework.easyconfig.style import check_easyconfigs_style @@ -52,9 +53,19 @@ def test_style_conformance(self): specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) specs = sorted(specs) + self.mock_stderr(True) + self.mock_stdout(True) result = check_easyconfigs_style(specs) + stderr, stdout = self.get_stderr(), self.get_stdout() + self.mock_stderr(False) + self.mock_stdout(False) - self.assertEqual(result, 0, "Found code style errors (and/or warnings): %s" % result) + error_msg = '\n'.join([ + "There shouldn't be any code style errors (and/or warnings), found %d:" % result, + stdout, + stderr, + ]) + self.assertEqual(result, 0, error_msg) def suite(loader=None): From b7b67a23ecae88e4b435d5cd91268eead04c922c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:19:22 +0100 Subject: [PATCH 163/528] {lang}[foss/2021b] numba v0.54.1 w/ Python 3.9.6 (on top of LLVM 12.0.1) --- .../n/numba/llvmlite-0.37.0_fix-LLVM-12.patch | 95 +++++++ .../n/numba/numba-0.54.1-foss-2021b.eb | 58 ++++ .../n/numba/numba-0.54.1_fix-numpy-1.21.patch | 251 ++++++++++++++++++ 3 files changed, 404 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch new file mode 100644 index 00000000000..444d8c6fc42 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch @@ -0,0 +1,95 @@ +see https://github.com/numba/llvmlite/issues/688 + +changes from https://github.com/numba/llvmlite/pull/802 backported to llvmlite 0.37.0 + +From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001 +From: Richard Barnes +Date: Wed, 1 Dec 2021 10:29:08 -0700 +Subject: [PATCH] Enable LLVM-12 and LLVM-13 + +--- + ffi/build.py | 5 ++--- + ffi/targets.cpp | 2 ++ + llvmlite/tests/test_binding.py | 19 ++++++++++++++++--- + 3 files changed, 20 insertions(+), 6 deletions(-) + +diff --git a/ffi/build.py b/ffi/build.py +index 6408bf5f..95e33c64 100755 +--- a/ffi/build.py ++++ b/ffi/build.py +@@ -162,9 +162,8 @@ def main_posix(kind, library_ext): + print(msg) + print(warning + '\n') + else: +- +- if not out.startswith('11'): +- msg = ("Building llvmlite requires LLVM 11.x.x, got " ++ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')): ++ msg = ("Building llvmlite requires LLVM 11-13.x.x, got " + "{!r}. Be sure to set LLVM_CONFIG to the right executable " + "path.\nRead the documentation at " + "http://llvmlite.pydata.org/ for more information about " + +--- llvmlite-0.37.0/ffi/targets.cpp.orig 2021-12-15 16:43:02.794869270 +0100 ++++ llvmlite-0.37.0/ffi/targets.cpp 2021-12-15 16:43:26.665056528 +0100 +@@ -232,7 +232,9 @@ + rm = Reloc::DynamicNoPIC; + + TargetOptions opt; ++#if LLVM_VERSION_MAJOR < 12 + opt.PrintMachineCode = PrintMC; ++#endif + + bool jit = JIT; + +diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py +index 80495787..fee2372a 100644 +--- a/llvmlite/tests/test_binding.py ++++ b/llvmlite/tests/test_binding.py +@@ -18,6 +18,16 @@ + from llvmlite.tests import TestCase + + ++def clean_string_whitespace(x: str) -> str: ++ # Remove trailing whitespace from the end of each line ++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) ++ # Remove intermediate blank lines ++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) ++ # Remove extraneous whitespace from the beginning and end of the string ++ x = x.strip() ++ return x ++ ++ + # arvm7l needs extra ABI symbols to link successfully + if platform.machine() == 'armv7l': + llvm.load_library_permanently('libgcc_s.so.1') +@@ -158,7 +168,7 @@ def no_de_locale(): + target triple = "unknown-unknown-unknown" + target datalayout = "" + +-define i32 @"foo"() ++define i32 @"foo"() + { + "<>!*''#": + ret i32 12345 +@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self): + bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) + bd.ret(ir.Constant(ir.IntType(32), 12345)) + asm = str(mod) +- self.assertEqual(asm, asm_nonalphanum_blocklabel) ++ self.assertEqual( ++ clean_string_whitespace(asm), ++ clean_string_whitespace(asm_nonalphanum_blocklabel) ++ ) + + def test_global_context(self): + gcontext1 = llvm.context.get_global_context() +@@ -509,7 +522,7 @@ def test_set_option(self): + def test_version(self): + major, minor, patch = llvm.llvm_version_info + # one of these can be valid +- valid = [(11,)] ++ valid = [(11,), (12,), (13,)] + self.assertIn((major,), valid) + self.assertIn(patch, range(10)) + diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb new file mode 100644 index 00000000000..4a12631542f --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.54.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('LLVM', '12.0.1'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.37.0', { + 'patches': ['llvmlite-0.37.0_fix-LLVM-12.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '6392b870cd018ec0c645d6bbb918d6aa0eeca8c62674baaee30862d6b6865b15', # llvmlite-0.37.0.tar.gz + 'bcdc530cfd087e8a9f68a73a80fe73f12c7b2adfdb51ded70cd2f4c404846298', # llvmlite-0.37.0_fix-LLVM-12.patch + ], + }), + (name, version, { + 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + 'f9dfc803c864edcc2381219b800abf366793400aea55e26d4d5b7d953e14f43f', # numba-0.54.1.tar.gz + 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199', # numba-0.54.1_fix-numpy-1.21.patch + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch b/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch new file mode 100644 index 00000000000..f15a14ee48e --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch @@ -0,0 +1,251 @@ +fix compatibility with numpy 1.21 +extracted from https://github.com/numba/numba/pull/7483 + +--- numba-0.54.1/setup.py.orig 2021-12-15 15:49:05.785690139 +0100 ++++ numba-0.54.1/setup.py 2021-12-15 15:49:09.255689514 +0100 +@@ -23,7 +23,7 @@ + max_python_version = "3.10" # exclusive + min_numpy_build_version = "1.11" + min_numpy_run_version = "1.17" +-max_numpy_run_version = "1.21" ++max_numpy_run_version = "1.22" + min_llvmlite_version = "0.37.0rc1" + max_llvmlite_version = "0.38" + +--- numba-0.54.1/numba/__init__.py.orig 2021-10-08 19:12:54.197672600 +0200 ++++ numba-0.54.1/numba/__init__.py 2021-12-15 15:57:05.995560177 +0100 +@@ -134,8 +134,8 @@ + + if numpy_version < (1, 17): + raise ImportError("Numba needs NumPy 1.17 or greater") +- elif numpy_version > (1, 20): +- raise ImportError("Numba needs NumPy 1.20 or less") ++ elif numpy_version > (1, 21): ++ raise ImportError("Numba needs NumPy 1.21 or less") + + try: + import scipy + + +From cff3dd6f92286fd8621a902d6595b65208e90013 Mon Sep 17 00:00:00 2001 +From: Sebastian Berg +Date: Thu, 30 Sep 2021 14:27:01 -0500 +Subject: [PATCH 6/8] BUG: Support the fastcall mechanism for NumPy's ufunc + methods + +This is a start to support NumPy 1.21 use of FASTCALL methods +in ufuncs. There are probably better ways to achieve this support. + +NumPy further uses `tp_vectorcall_offset` on newer versions. This +PR does not add support for this (meaning that a DUfunc will be +unnecessarily slow on NumPy >=1.21 when kwargs are used). +--- + numba/np/ufunc/_internal.c | 99 +++++++++++++++++++++++++++++++++++++- + 1 file changed, 97 insertions(+), 2 deletions(-) + +diff --git a/numba/np/ufunc/_internal.c b/numba/np/ufunc/_internal.c +index d3ca1319b6..600014df55 100644 +--- a/numba/np/ufunc/_internal.c ++++ b/numba/np/ufunc/_internal.c +@@ -276,6 +276,7 @@ static PyMemberDef dufunc_members[] = { + */ + + static struct _ufunc_dispatch { ++ /* Note that the following may also hold `_PyCFunctionFastWithKeywords` */ + PyCFunctionWithKeywords ufunc_reduce; + PyCFunctionWithKeywords ufunc_accumulate; + PyCFunctionWithKeywords ufunc_reduceat; +@@ -286,7 +287,7 @@ static struct _ufunc_dispatch { + } ufunc_dispatch; + + static int +-init_ufunc_dispatch(void) ++init_ufunc_dispatch(int *numpy_uses_fastcall) + { + int result = 0; + PyMethodDef * crnt = PyUFunc_Type.tp_methods; +@@ -329,6 +330,16 @@ init_ufunc_dispatch(void) + result = -1; /* Unknown method */ + } + if (result < 0) break; ++ ++ /* Check whether NumPy uses fastcall (ufunc.at never uses it) */ ++ if (!strncmp(crnt_name, "at", 3)) { ++ if (*numpy_uses_fastcall == -1) { ++ *numpy_uses_fastcall = crnt->ml_flags & METH_FASTCALL; ++ } ++ else if (*numpy_uses_fastcall != (crnt->ml_flags & METH_FASTCALL)) { ++ return -1; ++ } ++ } + } + if (result == 0) { + /* Sanity check. */ +@@ -344,6 +355,7 @@ init_ufunc_dispatch(void) + return result; + } + ++ + static PyObject * + dufunc_reduce(PyDUFuncObject * self, PyObject * args, PyObject *kws) + { +@@ -368,6 +380,47 @@ dufunc_outer(PyDUFuncObject * self, PyObject * args, PyObject *kws) + return ufunc_dispatch.ufunc_outer((PyObject*)self->ufunc, args, kws); + } + ++ ++/* ++ * The following are the vectorcall versions of the above, since NumPy ++ * uses the FASTCALL/Vectorcall protocol starting with version 1.21. ++ * The only NumPy versions supporting vectorcall use Python 3.7 or higher. ++ */ ++static PyObject * ++dufunc_reduce_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_reduce)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++static PyObject * ++dufunc_reduceat_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_reduceat)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ ++static PyObject * ++dufunc_accumulate_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_accumulate)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ ++static PyObject * ++dufunc_outer_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_outer)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ + #if NPY_API_VERSION >= 0x00000008 + static PyObject * + dufunc_at(PyDUFuncObject * self, PyObject * args) +@@ -568,6 +621,41 @@ static struct PyMethodDef dufunc_methods[] = { + {NULL, NULL, 0, NULL} /* sentinel */ + }; + ++ ++/* ++ * If Python is new enough, NumPy may use fastcall. In that case we have to ++ * also use fastcall for simplicity and speed. ++ */ ++static struct PyMethodDef dufunc_methods_fast[] = { ++ {"reduce", ++ (PyCFunction)dufunc_reduce_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"accumulate", ++ (PyCFunction)dufunc_accumulate_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"reduceat", ++ (PyCFunction)dufunc_reduceat_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"outer", ++ (PyCFunction)dufunc_outer_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL}, ++#if NPY_API_VERSION >= 0x00000008 ++ {"at", ++ (PyCFunction)dufunc_at, ++ METH_VARARGS, NULL}, ++#endif ++ {"_compile_for_args", ++ (PyCFunction)dufunc__compile_for_args, ++ METH_VARARGS | METH_KEYWORDS, ++ "Abstract method: subclasses should overload _compile_for_args() to compile the ufunc at the given arguments' types."}, ++ {"_add_loop", ++ (PyCFunction)dufunc__add_loop, ++ METH_VARARGS, ++ NULL}, ++ {NULL, NULL, 0, NULL} /* sentinel */ ++}; ++ ++ + static PyObject * + dufunc_getfrozen(PyDUFuncObject * self, void * closure) + { +@@ -681,8 +769,15 @@ MOD_INIT(_internal) + return MOD_ERROR_VAL; + + PyDUFunc_Type.tp_new = PyType_GenericNew; +- if (init_ufunc_dispatch() <= 0) ++ ++ int numpy_uses_fastcall = -1; ++ if (init_ufunc_dispatch(&numpy_uses_fastcall) <= 0) + return MOD_ERROR_VAL; ++ ++ if (numpy_uses_fastcall) { ++ PyDUFunc_Type.tp_methods = dufunc_methods_fast; ++ } ++ + if (PyType_Ready(&PyDUFunc_Type) < 0) + return MOD_ERROR_VAL; + Py_INCREF(&PyDUFunc_Type); + +From 4df2640b60804f1462e2f48b72f744005ed6ec9a Mon Sep 17 00:00:00 2001 +From: Stuart Archibald +Date: Fri, 15 Oct 2021 15:23:53 +0100 +Subject: [PATCH 7/8] Add suggested fix for detecting ufunc.at + +As title. +--- + numba/np/ufunc/_internal.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/numba/np/ufunc/_internal.c b/numba/np/ufunc/_internal.c +index 600014df55..d3e19b1cdc 100644 +--- a/numba/np/ufunc/_internal.c ++++ b/numba/np/ufunc/_internal.c +@@ -332,7 +332,7 @@ init_ufunc_dispatch(int *numpy_uses_fastcall) + if (result < 0) break; + + /* Check whether NumPy uses fastcall (ufunc.at never uses it) */ +- if (!strncmp(crnt_name, "at", 3)) { ++ if (strncmp(crnt_name, "at", 3) != 0) { + if (*numpy_uses_fastcall == -1) { + *numpy_uses_fastcall = crnt->ml_flags & METH_FASTCALL; + } + +From 635e05661b5d715bd8a9cb9448bd24930f693c38 Mon Sep 17 00:00:00 2001 +From: Stuart Archibald +Date: Tue, 16 Nov 2021 12:06:11 +0000 +Subject: [PATCH 8/8] Skip NaT input on np.median test for np=1.21. + +As title. See: https://github.com/numpy/numpy/issues/20376 +--- + numba/tests/test_array_reductions.py | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/numba/tests/test_array_reductions.py b/numba/tests/test_array_reductions.py +index de0d445fe6..a5763a753b 100644 +--- a/numba/tests/test_array_reductions.py ++++ b/numba/tests/test_array_reductions.py +@@ -686,8 +686,11 @@ def _do_check_nptimedelta(self, pyfunc, arr): + np.random.shuffle(arr) + self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) + # Test with a NaT +- arr[arr.size // 2] = 'NaT' +- self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) ++ if numpy_version != (1, 21) and 'median' not in pyfunc.__name__: ++ # There's problems with NaT handling in "median" on at least NumPy ++ # 1.21.{3, 4}. See https://github.com/numpy/numpy/issues/20376 ++ arr[arr.size // 2] = 'NaT' ++ self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) + if 'median' not in pyfunc.__name__: + # Test with (val, NaT)^N (and with the random NaT from above) + # use a loop, there's some weird thing/bug with arr[1::2] = 'NaT' From 53685dc4be68acdc496e4c3dc96308926e719478 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Dec 2021 03:13:07 +0200 Subject: [PATCH 164/528] fix checksum of annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb --- ...nnovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb index 9d250df45b7..67616ff591d 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb @@ -1,23 +1,21 @@ easyblock = 'Tarball' name = 'annovar' -# Unconventional version is taken from the upstream site -# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ -version = '20191024' +version = '20191024' # version reported by `annotate_variation.pl -h` versionsuffix = '-Perl-%(perlver)s' homepage = 'http://annovar.openbioinformatics.org/en/latest/' -description = """ANNOVAR is an efficient software tool to utilize update-to-date information -to functionally annotate genetic variants detected from diverse genomes (including human +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Registration required for download -# http://download.openbioinformatics.org/annovar_download_form.php +# http://www.openbioinformatics.org/annovar/annovar_download_form.php # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] +checksums = ['78a362a3bd771e4ac46b280c6b52f0d8452f32f11e3812f5d7f85797d26ae799'] dependencies = [('Perl', '5.28.1')] @@ -26,12 +24,13 @@ modextrapaths = { } sanity_check_paths = { - 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], 'dirs': ["example", "humandb"], } sanity_check_commands = [ - 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', ] From 281e016d92ca1c16ccc96e7b7744a4499375dddc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Dec 2021 03:16:19 +0200 Subject: [PATCH 165/528] fix version of annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb --- ...nnovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb} | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/a/annovar/{annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb => annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb} (64%) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb similarity index 64% rename from easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb rename to easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb index 91bdfccb8ef..36f2f721a05 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb @@ -1,13 +1,9 @@ -# Toolchain updated to GCCcore-11.2 -# Downloaded tarball has same checksum as the one from 20191024 -# J. Sassmannshausen /NHS/GSTT +# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2 easyblock = 'Tarball' name = 'annovar' -# Unconventional version is taken from the upstream site -# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ -version = '20191024' +version = '20200607' # version reported by `annotate_variation.pl -h` versionsuffix = '-Perl-%(perlver)s' homepage = 'http://annovar.openbioinformatics.org/en/latest/' @@ -18,7 +14,7 @@ genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} # Registration required for download -# http://download.openbioinformatics.org/annovar_download_form.php +# http://www.openbioinformatics.org/annovar/annovar_download_form.php # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] @@ -30,12 +26,13 @@ modextrapaths = { } sanity_check_paths = { - 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], 'dirs': ["example", "humandb"], } sanity_check_commands = [ - 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', ] From f52443c9a464ade7b52bebcae1a05cbfb57ed81e Mon Sep 17 00:00:00 2001 From: alexandermichels Date: Wed, 15 Dec 2021 21:31:49 -0500 Subject: [PATCH 166/528] adding easyconfigs: CDO-1.9.10-gompi-2019b.eb --- .../c/CDO/CDO-1.9.10-gompi-2019b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb new file mode 100644 index 00000000000..c356f156e66 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('YAXT', '0.6.2'), + ('ecCodes', '2.17.0'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' From 939107805138eca044830b931385cf24d7fe26b5 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 15:43:52 +1050 Subject: [PATCH 167/528] style <- dep version fix --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index 3c93ab37e8c..fd37b7cc2b1 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.3', versionsuffix), + ('python-parasail', '1.2.2', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 2b3ce8302fb2b7b5508a7511ce8e79ff78b6b5b8 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:08:16 +1050 Subject: [PATCH 168/528] style <- dep version fix --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index fd37b7cc2b1..3c93ab37e8c 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.2', versionsuffix), + ('python-parasail', '1.2.3', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 1fd41967ef73d431b9ac80b5e660a78bb311b5d3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:37:51 +1050 Subject: [PATCH 169/528] version upgrade <- dep update to new versions --- .../p/parasail/parasail-2.4.3-GCC-10.3.0.eb | 27 ++++++++++++++++ .../python-parasail-1.2.4-foss-2021a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..b3298d8ce84 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.4.3' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6f0cddcaaf7c00573e62a3b081a09380cb022b2ed6a3a138108f8823775ca026'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb new file mode 100644 index 00000000000..752bd173d53 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From d634b25c0ca6068a80bcc992a02953c620693f0c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:40:34 +1050 Subject: [PATCH 170/528] version upgrade <- toolchain version upgrade to foss-2021a --- .../c/Cogent/Cogent-8.0.0-foss-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb new file mode 100644 index 00000000000..cc67b275bd1 --- /dev/null +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -0,0 +1,49 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'Cogent' +version = '8.0.0' + +homepage = 'https://github.com/Magdoll/Cogent' +description = """ +Cogent is a tool for reconstructing the coding genome using high-quality +full-length transcriptome sequences. It is designed to be used on Iso-Seq data +and in cases where there is no reference genome or the ref genome is highly +incomplete. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('networkx', '2.6.3'), + ('scikit-image', '0.18.3'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('python-parasail', '1.2.4'), + ('CapnProto', '0.9.1'), + ('minimap2', '2.20'), + ('Mash', '2.3'), + ('cDNA_Cupcake', '26.0.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/run_mash.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From df5f9d40fbaf89b5f031c2cc359a70c678ec402c Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 16:22:41 +1030 Subject: [PATCH 171/528] Delete Cogent-8.0.0-foss-2020a-Python-3.8.2.eb --- .../Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 52 ------------------- 1 file changed, 52 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3c93ab37e8c..00000000000 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,52 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'Cogent' -version = '8.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Magdoll/Cogent' -description = """ -Cogent is a tool for reconstructing the coding genome using high-quality -full-length transcriptome sequences. It is designed to be used on Iso-Seq data -and in cases where there is no reference genome or the ref genome is highly -incomplete. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('networkx', '2.4', versionsuffix), - ('scikit-image', '0.17.1', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.3', versionsuffix), - ('CapnProto', '0.8.0'), - ('minimap2', '2.17'), - ('Mash', '2.2'), - ('cDNA_Cupcake', '24.2.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/run_mash.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'Cogent'} - -moduleclass = 'bio' From 17fb73ef99df37082d6151b529082d330b48876a Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 17:10:04 +1050 Subject: [PATCH 172/528] more sanity checks + --- .../easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index cc67b275bd1..697c1e0ae47 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -42,8 +42,17 @@ use_pip = True sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/run_mash.py'], + 'files': ['bin/%s' % x for x in ['run_mash.py', + 'process_kmer_to_graph.py', + 'reconstruct_contig.py'] + ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'run_mash.py -h', + 'process_kmer_to_graph.py -h', + 'reconstruct_contig.py -h', +] + moduleclass = 'bio' From 27dceec445af42dd2c56a96879092c864d520bc2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 18:41:28 +1050 Subject: [PATCH 173/528] adding easyconfigs: python-pulp-2.5.1-foss-2021a.eb --- .../python-pulp-2.5.1-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb new file mode 100644 index 00000000000..b715a09d17e --- /dev/null +++ b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'python-pulp' +version = '2.5.1' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] +sources = ['PuLP-%(version)s.tar.gz'] +checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'pulp'} + +moduleclass = 'tools' From 5cbb63bdea9239d135addfeed5a674fa55dbfd7d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 18:45:57 +1050 Subject: [PATCH 174/528] debug <- pip dep + & module import fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 697c1e0ae47..147ae621c04 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -35,6 +35,7 @@ dependencies = [ ('minimap2', '2.20'), ('Mash', '2.3'), ('cDNA_Cupcake', '26.0.0'), + ('python-pulp', '2.5.1'), ] download_dep_fail = True @@ -55,4 +56,6 @@ sanity_check_commands = [ 'reconstruct_contig.py -h', ] +options = {'modulename': 'Cogent'} + moduleclass = 'bio' From 6c79b51952978b9d729bdd31634e3ff19d9030db Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 19:25:03 +1050 Subject: [PATCH 175/528] v8.0.0 url fix --- .../easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 147ae621c04..bca8f6f7144 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -18,9 +18,14 @@ incomplete. toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] +# standard URL for Cogent +# source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +# sources = ['v%(version)s.tar.gz'] + +# v8.0.0 bug fix URL +source_urls = ['https://github.com/Magdoll/Cogent/archive'] +sources = ['c44054bf88b94e77f475c3a6907da7609aee60ad.zip'] +checksums = ['90c8a810478d5d7b31441c1b818547e7de0aaf6a02001f36dcb618d3d10e1d48'] dependencies = [ ('Python', '3.9.5'), From 3cce1334d9e0ed4284af35ad3e15e08b7172782c Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 16 Dec 2021 10:22:06 +0100 Subject: [PATCH 176/528] adding easyconfigs: Armadillo-10.7.5-foss-2021a.eb --- .../Armadillo/Armadillo-10.7.5-foss-2021a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb new file mode 100644 index 00000000000..db49e1ec8f1 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = "10.7.5" + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5d0d9fd6b34efcba6a6fceff54c0d2d13fcbe915d7af8a30c5e72cf317d2094f'] + +dependencies = [ + ('Boost', '1.76.0'), + ('arpack-ng', '3.8.0'), +] + +builddependencies = [('CMake', '3.20.1')] + +moduleclass = 'numlib' From 841d0789fac68f0ada394590f91f1e60442f39be Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 21:17:06 +1050 Subject: [PATCH 177/528] dep <- optional + --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a747217d2f7 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' From bba7c934a8984bcb6fe1c9a7c2e26d0529269d42 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 16 Dec 2021 10:37:45 +0000 Subject: [PATCH 178/528] Improve sanity checks Ensure `sanity_check_paths` checks all copied files Use `mpi_cmd_prefix` template instead of hardcoding `mpirun` in the sanity check Co-authored-by: Alex Domingo --- .../easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb index de135d9fb64..ffb5f8bc711 100644 --- a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb @@ -24,15 +24,17 @@ prebuildopts = "sed -i '1d' Makefile && " # -fallow-argument-mismatch needed for GCC 10+ buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' -files_to_copy = [([name], 'bin'), 'Test-*', 'LICENSE', 'README.md'] +local_tests = ["Test-%s" % x for x in ['QE', 'RTA', 'VASP']] + +files_to_copy = [([name], 'bin'), (['LICENSE', 'README.md'], 'share')] + local_tests sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': [], + 'dirs': ['share'] + local_tests, } sanity_check_commands = [ - "cd %%(builddir)s/*%%(namelower)s*/Test-%s && mpirun -n %%(parallel)s %%(name)s" % x for x in ['QE', 'RTA', 'VASP'] + "cd %%(builddir)s/*%%(namelower)s*/%s && %%(mpi_cmd_prefix)s %%(name)s" % x for x in local_tests ] moduleclass = 'phys' From 61e172b2f7fe1648f75c61c7e9b83c243f734d45 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 16 Dec 2021 13:45:54 +0200 Subject: [PATCH 179/528] adding easyconfigs: genozip-13.0.5-GCCcore-11.2.0.eb --- .../genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..222b97ad9d2 --- /dev/null +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'genozip' +version = '13.0.5' + + +homepage = 'https://genozip.com' +description = """Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others. Documentation: genozip.com. Support: support@genozip.com""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/divonlan/genozip/archive/refs/tags/'] +sources = ['%(name)s-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.37') +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_commands = ['genozip --help'] + +sanity_check_paths = { + 'files': ['bin/genocat', 'bin/genozip', 'bin/genounzip', 'bin/genols'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' \ No newline at end of file From dc3abb935bde93912b597f0d0db3f868d3918d2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 12:54:13 +0100 Subject: [PATCH 180/528] add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot --- .../r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 6 +++- .../r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 6 +++- .../Rust-1.52.1_sysroot-fix-interpreter.patch | 30 +++++++++++++++++++ .../r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 6 +++- 4 files changed, 45 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 2e64f844463..1de0bc61268 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index 11974f2841f..ec7ed7d0232 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch new file mode 100644 index 00000000000..058dc409569 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch @@ -0,0 +1,30 @@ +Use patchelf to fix interpreter of binaries that are used during Rust bootstrap procedure +when EasyBuild is configured to build in an alternate sysroot + +This fixes problems like due to a clash with the interpreter from the host, and a more recent libc.so.6 that's picked up +from the alternate sysroot: +error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /tmp/easybuild/build/Rust/1.52.1/GCCcore-10.3.0/rustc-1.52.1-src/build/bootstrap/debug/deps/libproc_macro_error_attr-fbfef320d848b049.so) + +author: Kenneth Hoste (HPC-UGent) + +--- rustc-1.42.0-src/src/bootstrap/bootstrap.py.orig 2020-03-09 22:11:17.000000000 +0000 ++++ rustc-1.42.0-src/src/bootstrap/bootstrap.py 2021-12-16 10:34:25.100100855 +0000 +@@ -446,6 +446,18 @@ + if ostype != "Linux": + return + ++ sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if sysroot and not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' ++ file_b_out = subprocess.check_output(['file', '-b', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*, interpreter ([^,]*),.*') ++ res = regex.match(file_b_out) ++ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ + if not os.path.exists("/etc/NIXOS"): + return + if os.path.exists("/lib"): diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index efafcecfca8..5e8146115eb 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + 'ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976', # rustc-1.54.0-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.37'), From e66ddb34eb8d06402e007b6d0313fb4f471e3a96 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:30:53 +1050 Subject: [PATCH 181/528] dep <- optional + --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb new file mode 100644 index 00000000000..dafbf0502d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.0 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From aa014e179b0f4cd73cac500cdc12102061530a5a Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 23:18:10 +1030 Subject: [PATCH 182/528] Delete SEPP-4.5.0-foss-2021a.eb --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb deleted file mode 100644 index dafbf0502d1..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.5.0 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.5.0' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.9.5'), - ('DendroPy', '4.5.2'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From 273197e32605f1ac8db18d150a9725389618fd45 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:40:10 +1050 Subject: [PATCH 183/528] dep <- optional + --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb new file mode 100644 index 00000000000..dafbf0502d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.0 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 50742049093fe9b30827a1c82b7ee556ac986a01 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:51:26 +1050 Subject: [PATCH 184/528] dep <- optional + --- .../s/SEPP/SEPP-4.3.10-foss-2020a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb new file mode 100644 index 00000000000..455f30dabf2 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.3.10 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.3.10' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.8.2'), + ('DendroPy', '4.4.0'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', + 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From cb60a58d5292b94847c9201ff81912b5206560f2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:03:45 +1050 Subject: [PATCH 185/528] adding easyconfigs: SEPP-4.5.0-foss-2021b.eb, DendroPy-4.5.2-GCCcore-11.2.0.eb --- .../DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb | 43 ++++++++++++++++++ .../s/SEPP/SEPP-4.5.0-foss-2021b.eb | 44 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f7e6b5f85b2 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb new file mode 100644 index 00000000000..a531a1e0a72 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From b48f4913dd145fdd6786a43270ecffba4df3ae2c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:09:33 +1050 Subject: [PATCH 186/528] dep <- optional + --- .../PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index d033ab417bb..235d37e2877 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -29,6 +29,15 @@ dependencies = [ ('DendroPy', '4.4.0'), ('matplotlib', '3.2.1', versionsuffix), ('Seaborn', '0.10.1', versionsuffix), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.2'), + ('MUSCLE', '3.8.31'), + ('MAFFT', '7.470', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667', '-i86linux32'), + ('DIAMOND', '2.0.4'), ] use_pip = True From ac38be6ac8bea48543e0dd5fa76c37ec6121940b Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:27:18 +1050 Subject: [PATCH 187/528] debug <- dep version style fix --- .../SEPP-4.3.10-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ede3aa68bef --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.3.10 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.3.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['24d8d410138563017e6f2f1263d5e34427f5bbddb875b72a036f7c879cef203b'] + +dependencies = [ + ('Python', '3.8.2'), + ('DendroPy', '4.4.0'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', + 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 92f253a8f975a1b58106f9637c04310e6d7bc0b6 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 00:09:09 +1030 Subject: [PATCH 188/528] Delete SEPP-4.3.10-foss-2020a.eb --- .../s/SEPP/SEPP-4.3.10-foss-2020a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb deleted file mode 100644 index 455f30dabf2..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.3.10 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.3.10' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.8.2'), - ('DendroPy', '4.4.0'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', - 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From fbfcb4f4f5b2e7ab0116b343fbd7c10e26033ebe Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:35:10 +1050 Subject: [PATCH 189/528] debug <- dep version style fix --- easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb index dafbf0502d1..760c7acd3f1 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -17,6 +17,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'smirarab' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['b464b5f3e51c2c52e85f6fe51cba80746199472f117a88a80213bc457f867455'] dependencies = [ ('Python', '3.9.5'), From 135279b3bd30cf0e2a8e8ee7f56d7833a76b43c2 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 00:17:53 +1030 Subject: [PATCH 190/528] Delete SEPP-4.5.0-foss-2021b.eb --- .../s/SEPP/SEPP-4.5.0-foss-2021b.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb deleted file mode 100644 index a531a1e0a72..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.5.1 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.5.0' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.9.6'), - ('DendroPy', '4.5.2'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From e4da8b6e0a7e7953e90f23d35e426f8ddc8c8880 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:44:21 +1050 Subject: [PATCH 191/528] debug <- dep version & style fix --- .../s/SEPP/SEPP-4.5.1-foss-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb new file mode 100644 index 00000000000..7c772367fad --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.1' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b'] + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 2b262745cc9b0c6918f6866b1cb581675e7cd6a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 14:56:51 +0100 Subject: [PATCH 192/528] retain version in filename for cromwell sources --- .../c/cromwell/cromwell-56-Java-11.eb | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb index 7e167fc41e1..4e68ade3eeb 100644 --- a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb +++ b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb @@ -11,22 +11,21 @@ toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s/'] sources = [ - { - 'download_filename': '%(name)s-%(version)s.jar', - 'filename': '%(name)s.jar', - }, - { - 'download_filename': 'womtool-%(version)s.jar', - 'filename': 'womtool.jar', - }, + '%(name)s-%(version)s.jar', + 'womtool-%(version)s.jar', ] checksums = [ - '955502419cfec2a687ea56f7f4a433b395af09c9a078e60a5676c7ad56c3965d', # cromwell.jar - '0f561c0d387412715f1f688ad5ae7cd4d8af3dc8d68c69ae9fc35ecae4f481c6', # womtool.jar + '955502419cfec2a687ea56f7f4a433b395af09c9a078e60a5676c7ad56c3965d', # cromwell-56.jar + '0f561c0d387412715f1f688ad5ae7cd4d8af3dc8d68c69ae9fc35ecae4f481c6', # womtool-56.jar ] dependencies = [('Java', '11')] +postinstallcmds = [ + "mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar", + "mv %(installdir)s/womtool-%(version)s.jar %(installdir)s/womtool.jar", +] + sanity_check_paths = { 'files': ['%(name)s.jar', 'womtool.jar'], 'dirs': [], From 4e64f4747cca8dc7577f70e1b40d1a45369957e3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 01:12:51 +1050 Subject: [PATCH 193/528] debug <- dep version fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 235d37e2877..d7359439626 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -33,10 +33,10 @@ dependencies = [ ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), ('MAFFT', '7.470', '-with-extensions'), - ('SEPP', '4.5.0'), + ('SEPP', '4.3.10'), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667', '-i86linux32'), + ('USEARCH', '11.0.667-i86linux32', '', True), ('DIAMOND', '2.0.4'), ] From 5be1d8f38e426d71bb1b377e8a2c3ad8dbb6b547 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 01:48:28 +1050 Subject: [PATCH 194/528] debug <- dep version fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index d7359439626..7ab31f9c348 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -33,7 +33,7 @@ dependencies = [ ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), ('MAFFT', '7.470', '-with-extensions'), - ('SEPP', '4.3.10'), + ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), ('USEARCH', '11.0.667-i86linux32', '', True), From 8d11780cb08cc5b492b30ab9264d452e096ec0d1 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 01:53:11 +1030 Subject: [PATCH 195/528] debug <- dep version conflict fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 7ab31f9c348..98b660aba06 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -32,10 +32,10 @@ dependencies = [ ('FastTree', '2.1.11'), ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), - ('MAFFT', '7.470', '-with-extensions'), + ('MAFFT', '7.453', '-with-extensions'), ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), - ('BLAST+', '2.11.0'), + ('BLAST+', '2.10.1'), ('USEARCH', '11.0.667-i86linux32', '', True), ('DIAMOND', '2.0.4'), ] From feb24eca9013ce33c659d5a80a77f6ee6e965102 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 16:41:19 +0100 Subject: [PATCH 196/528] add Brotli-python dependency for FMPy --- easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb index 4e8249a47d2..5af7f211e5a 100644 --- a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb +++ b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb @@ -20,7 +20,7 @@ dependencies = [ ('IPython', '7.25.0'), ('plotly.py', '5.1.0'), ('Flask', '1.1.4'), - ('Brotli', '1.0.9'), + ('Brotli-python', '1.0.9'), ] use_pip = True From 151c1924e39b6334b2f09cfd2fcdfabc36058f23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 17:06:17 +0100 Subject: [PATCH 197/528] trivial style fixes for genozip easyconfig --- .../g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb index 222b97ad9d2..16182a13684 100644 --- a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -3,9 +3,8 @@ easyblock = 'ConfigureMake' name = 'genozip' version = '13.0.5' - homepage = 'https://genozip.com' -description = """Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others. Documentation: genozip.com. Support: support@genozip.com""" +description = "Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others." toolchain = {'name': 'GCCcore', 'version': '11.2.0'} @@ -20,11 +19,11 @@ skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' -sanity_check_commands = ['genozip --help'] - sanity_check_paths = { 'files': ['bin/genocat', 'bin/genozip', 'bin/genounzip', 'bin/genols'], 'dirs': ['bin'], } -moduleclass = 'bio' \ No newline at end of file +sanity_check_commands = ['genozip --help'] + +moduleclass = 'bio' From 13c00d14022ed0b41959bea28dbaa73b61492d83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 17:24:15 +0100 Subject: [PATCH 198/528] add missing SHA256 checksum for genozip --- easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb index 16182a13684..0c6be10dfe5 100644 --- a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/divonlan/genozip/archive/refs/tags/'] sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['be2d5cbe1f5f84c2dc1a1d580361fc7f22a14ece4dac545ca2750ca07d49fac3'] builddependencies = [ ('binutils', '2.37') From 3a87d3bbb19bbbd73703ecaa39d4920306c130d4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Dec 2021 23:02:00 +0000 Subject: [PATCH 199/528] White space removed --- easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb index af597f02e72..1034b4e9a44 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb @@ -28,7 +28,7 @@ dependencies = [ ('SAMtools', '1.14'), ] -sanity_check_commands = [ 'bismark --help'] +sanity_check_commands = ['bismark --help'] sanity_check_paths = { 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', From ff0f39a79f3d9b563a76dcaf745461f90a1f56f2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 00:59:18 +0100 Subject: [PATCH 200/528] fix formatting in SEPP-4.5.1-foss-2021b.eb --- easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb index 7c772367fad..5fb5811a69f 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb @@ -30,10 +30,7 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] +local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py'] sanity_check_paths = { 'files': ['bin/%s' % f for f in local_bin_files], From 076ed7913ae4a3a7b1ecdee6130f39ae9953c1f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 01:04:04 +0100 Subject: [PATCH 201/528] use dendropy.org as homepage of DendroPy --- .../easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb index f7e6b5f85b2..c15219fd20d 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ easyblock = 'PythonPackage' name = 'DendroPy' version = '4.5.2' -homepage = 'https://pypi.python.org/pypi/DendroPy/' +homepage = 'https://dendropy.org/' description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.""" From af96361544c8d8847e2a569bfcf654491081474a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 01:45:18 +0100 Subject: [PATCH 202/528] downgrade dependency on ecCodes to v2.15.0 --- easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb index c356f156e66..bf08b255127 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb @@ -17,7 +17,7 @@ dependencies = [ ('HDF5', '1.10.5'), ('netCDF', '4.7.1'), ('YAXT', '0.6.2'), - ('ecCodes', '2.17.0'), + ('ecCodes', '2.15.0'), ] configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" From f5f305be88682664f277b8d4d26c70f6a6420d96 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 14:19:10 +1030 Subject: [PATCH 203/528] Update easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb Co-authored-by: Alex Domingo --- .../easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb index b715a09d17e..1f225063c2a 100644 --- a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb @@ -4,7 +4,7 @@ easyblock = 'PythonPackage' -name = 'python-pulp' +name = 'PuLP' version = '2.5.1' homepage = 'https://github.com/coin-or/pulp' From 93ef23c9c20bd0b2c4faa0a1aeb865b8ab81cdc9 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 14:57:26 +1050 Subject: [PATCH 204/528] dep <- optional packages + --- .../p/PuLP/PuLP-2.5.1-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb new file mode 100644 index 00000000000..6c0e40a7a24 --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -0,0 +1,37 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.5.1' + +homepage = 'https://pypi.org/project/PuLP' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] +sources = ['PuLP-%(version)s.tar.gz'] +checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] + +dependencies = [ + ('Python', '3.9.5'), + ('GLPK', '5.0'), + ('Cbc', '2.10.5'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' From d113c31ef660efc8ad3eb08206a2eb78dbff4246 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 14:38:15 +1030 Subject: [PATCH 205/528] Delete python-pulp-2.5.1-foss-2021a.eb --- .../python-pulp-2.5.1-foss-2021a.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb deleted file mode 100644 index 1f225063c2a..00000000000 --- a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb +++ /dev/null @@ -1,35 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'PuLP' -version = '2.5.1' - -homepage = 'https://github.com/coin-or/pulp' -description = """ -PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and -call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to -solve linear problems. -""" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] -sources = ['PuLP-%(version)s.tar.gz'] -checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] - -dependencies = [ - ('Python', '3.9.5'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -options = {'modulename': 'pulp'} - -moduleclass = 'tools' From cfd6abf40cedfcfcbbe2a5c833e376b557f64bc1 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 16:44:29 +1050 Subject: [PATCH 206/528] adding easyconfigs: IQ-TREE-2.1.3-gompi-2021a.eb, LSD2-2.3-GCCcore-10.3.0.eb --- .../i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb | 48 +++++++++++++++++++ .../l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb | 38 +++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb new file mode 100644 index 00000000000..2bc6a28974f --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb @@ -0,0 +1,48 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.1.3' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-2.1.2_use_EB_LSD2.patch'] +checksums = [ + '38ec7cfa36bee9958aa806773156c445beac9f01082d3593188f20fbbbb06894', # v2.1.3.tar.gz + 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = ["iqtree2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8e7a2ffbb55 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.3' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + 'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649', # v.2.3.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From a0430d962fa6563b37da69519f0c581d768ad264 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:07:00 +1050 Subject: [PATCH 207/528] adding easyconfigs: MUSCLE-5.0.1428.eb --- .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb new file mode 100644 index 00000000000..6d7ae644e8c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v5 + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.0.1428' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/rcedgar/%(namelower)s/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5'] + +skipsteps = ['config', 'build'] + +if (OS_TYPE == 'Linux'): + files_to_copy = [(["binaries/%(namelower)s"], 'bin')] +elif (OS_TYPE == 'Windows'): + files_to_copy = [(["binaries/%(namelower)s.exe"], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' From 303575bbbf914b5a78130888379243c7719a6ac2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:29:54 +1050 Subject: [PATCH 208/528] dep <- optional + --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ .../t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb | 32 ++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ad1c23f20f5 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.36.1')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ebf9a1d24b8 --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [('binutils', '2.36.1', '', True)] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +moduleclass = 'bio' From 4adea9f3adb935cdbe3cce9f71f7423b87bc6d65 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:34:11 +1050 Subject: [PATCH 209/528] dep <- all version update --- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 7cdf357fcbf..4309976ceb3 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -29,6 +29,15 @@ dependencies = [ ('DendroPy', '4.5.2'), ('matplotlib', '3.4.2'), ('Seaborn', '0.11.2'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.3'), + ('MUSCLE', '5.0.1428', '', True), + ('MAFFT', '7.490', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667-i86linux32', '', True), + ('DIAMOND', '2.0.11'), ] use_pip = True From 5a502d3203802ae9b8b779de4a89cf0f2c5d99e2 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 17 Dec 2021 14:43:22 +0200 Subject: [PATCH 210/528] adding easyconfigs: PyTorch-1.10.0-fosscuda-2020b.eb, CMake-3.20.1-GCCcore-10.2.0.eb, expecttest-0.1.3-GCCcore-10.2.0.eb --- .../c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb | 32 +++++ .../expecttest-0.1.3-GCCcore-10.2.0.eb | 25 ++++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 120 ++++++++++++++++++ 3 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..16e8766c691 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'CMake' +version = '3.20.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f1808b9b00281df06c91dd7a021d7f52f724101000da7985a401678dfe035b0'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1e133b2aea1 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = "https://github.com/ezyang/expecttest" +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..af85117afc4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -0,0 +1,120 @@ +name = 'PyTorch' +version = '1.10.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_failing_ops_tests.patch', + 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch + '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', + # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch + '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-test-cond-cpu.patch + '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-vnni-detection.patch + '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch + 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_failing_ops_tests.patch + '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', + # PyTorch-1.10.0_skip_nan_tests_openblas.patch + '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), # Needs 3.20 or newer. + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('expecttest', '0.1.3'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 101b832f334ee053883b6eafb437a5ef14c6ea8e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 15:50:04 +0000 Subject: [PATCH 211/528] Bundle an installation of LAPACKE with FlexiBLAS, since LAPACKE is not (yet) supported by FlexiBLAS --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 34 +++++++++++++++++-- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index b0f9ad78754..27f3930cfd8 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'Bundle' + name = 'FlexiBLAS' version = '3.0.4' @@ -9,9 +11,9 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] +#source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] +#sources = [SOURCELOWER_TAR_GZ] +#checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] builddependencies = [ ('CMake', '3.20.1'), @@ -24,4 +26,30 @@ dependencies = [ ('OpenBLAS', '0.3.15'), ] +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ + -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ + -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', + #'postinstallcmds': ["mv %(installdir)s/include/*.h %(installdir)s/include/flexiblas"], + }), +] + +sanity_check_paths = { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], +} + moduleclass = 'lib' From 852d1f1815c33b22b0c5bc21ed105beddb0fb697 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 15:52:04 +0000 Subject: [PATCH 212/528] Linting --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index 27f3930cfd8..75ed9461123 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -11,10 +11,6 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -#source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -#sources = [SOURCELOWER_TAR_GZ] -#checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] - builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), # required for running the tests From 3a75d841fc2a96a73515fadd7cf8a22888ea85c2 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 17 Dec 2021 15:52:34 +0000 Subject: [PATCH 213/528] remove commented postinstallcmds --- easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index 75ed9461123..a7982e2cd57 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -39,7 +39,6 @@ components = [ 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', - #'postinstallcmds': ["mv %(installdir)s/include/*.h %(installdir)s/include/flexiblas"], }), ] From 63ea92df1480321f133d89f9cb308ae84b95c04a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 16:08:24 +0000 Subject: [PATCH 214/528] adding easyconfigs: EIGENSOFT-7.2.1-foss-2021a.eb --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb new file mode 100644 index 00000000000..946ae3d37a6 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 6.1.4 modified by: +# Adam Huffman +# The Francis Crick Institute +# 7.2.1 modified by: +# Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '7.2.1' + +homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/DReichLab/EIG/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +checksums = [ + 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz + 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch +] + +dependencies = [ + ('GSL', '2.7'), + ('Perl', '5.32.1'), +] + +start_dir = 'src' + +# Run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -llapacke $LIBS" && make install' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +fix_perl_shebang_for = ['bin/*.perl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' From d527a0c2ae1d136087fce7ea3f0c7416d6e4cf36 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 17 Dec 2021 17:53:16 +0100 Subject: [PATCH 215/528] Create Anaconda3-2021.11.eb --- .../a/Anaconda3/Anaconda3-2021.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb new file mode 100644 index 00000000000..6006859638b --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb @@ -0,0 +1,29 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, +# 2020.2, 2020.11, 2021.11 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2021.11' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': 'fedf9e340039557f7b5e8a8a86affa9d299f5e9820144bd7b92ae9f7ee08ac60', + '%(name)s-%(version)s-Linux-ppc64le.sh': '7eb6a95925ee756240818599f8dcbba7a155adfb05ef6cd5336aa3c083de65f3', + } +] + +moduleclass = 'lang' From 927d52a64162b619fdcbaa4904d22305052bf98e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:33:57 +0100 Subject: [PATCH 216/528] fix sanity checks of MetaPhlAn v3.0.9 --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index a6979c9e19d..1fc584f1503 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ download_dep_fail = True sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], - 'dirs': ['bin', 'lib'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } sanity_check_commands = [('%(namelower)s', '-h')] From b2860d89c9299176f4d468f9d9c4ced34426bbd4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:50:17 +0100 Subject: [PATCH 217/528] update homepage of PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 6c0e40a7a24..1e4b4485af4 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -7,7 +7,7 @@ easyblock = 'PythonPackage' name = 'PuLP' version = '2.5.1' -homepage = 'https://pypi.org/project/PuLP' +homepage = 'https://github.com/coin-or/pulp' description = """ PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to From 7b374c6e8b8c4718893052625d3e547f18e72170 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:50:47 +0100 Subject: [PATCH 218/528] simplify sources of PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 1e4b4485af4..9096fd0af07 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -17,8 +17,7 @@ solve linear problems. toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] -sources = ['PuLP-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] dependencies = [ From 2be430f794ab08db5a3d87c6d6033d10bbda83ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:51:22 +0100 Subject: [PATCH 219/528] disable usempi in PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 9096fd0af07..0192ade0554 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -15,7 +15,6 @@ solve linear problems. """ toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} sources = [SOURCE_TAR_GZ] checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] From 46ec6bc5dc5436e4e5ee1f5c458deee8d59eb638 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 02:50:20 +0100 Subject: [PATCH 220/528] replace MUSCLE v5.0.1428 binaries with compilation in GCCcore/10.3.0 --- .../MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb | 36 --------------- ...SCLE-5.0.1428_add-ver-counter-header.patch | 31 +++++++++++++ 3 files changed, 75 insertions(+), 36 deletions(-) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17d9c5626cd --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.0.1428' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_add-ver-counter-header.patch'] +checksums = [ + '59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5', # v5.0.1428.tar.gz + '129e3cd5cd7ae4d9819bbb36776275781e33c82410ee1e5d480b3de2df213931', # MUSCLE-5.0.1428_add-ver-counter-header.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('ccache', '4.2.1', '', True), +] + +start_dir = 'src' + +# Use build environment defined by EB +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" + +files_to_copy = [(['o/muscle5'], 'bin')] +postinstallcmds = ["cd %(installdir)s/bin && ln -s muscle5 muscle"] + +sanity_check_paths = { + 'files': ['bin/muscle', 'bin/muscle5'], + 'dirs': [], +} + +sanity_check_commands = [('muscle', '-h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb deleted file mode 100644 index 6d7ae644e8c..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v5 - -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = '5.0.1428' - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = SYSTEM - -source_urls = ['https://github.com/rcedgar/%(namelower)s/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5'] - -skipsteps = ['config', 'build'] - -if (OS_TYPE == 'Linux'): - files_to_copy = [(["binaries/%(namelower)s"], 'bin')] -elif (OS_TYPE == 'Windows'): - files_to_copy = [(["binaries/%(namelower)s.exe"], 'bin')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch new file mode 100644 index 00000000000..991310e87b9 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch @@ -0,0 +1,31 @@ +From dd9c3e921a5f06bbc8be7593eab4d6e3433b6f67 Mon Sep 17 00:00:00 2001 +From: Robert Edgar +Date: Wed, 10 Nov 2021 08:05:06 -0800 +Subject: [PATCH] Fix ../ver/counter.h issue + +--- + src/myutils.cpp | 2 +- + src/ver_counter.h | 1 + + 2 files changed, 2 insertions(+), 1 deletion(-) + create mode 100644 src/ver_counter.h + +diff --git a/src/myutils.cpp b/src/myutils.cpp +index 5a49b4e..e1bc0fd 100644 +--- a/src/myutils.cpp ++++ b/src/myutils.cpp +@@ -2055,7 +2055,7 @@ void Split(const string &Str, vector &Fields, char Sep) + void GetVersionString(string &s) + { + const int counter = +-#include "../ver/counter.h" ++#include "ver_counter.h" + ; + const char *Flags = "" + +diff --git a/src/ver_counter.h b/src/ver_counter.h +new file mode 100644 +index 0000000..4efaa29 +--- /dev/null ++++ b/src/ver_counter.h +@@ -0,0 +1 @@ ++1428 From 3df2e9f63588e1790712df95b19e26b1ee6ff494 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 18 Dec 2021 20:31:15 +1050 Subject: [PATCH 221/528] dep <- MUSCLE downgrade to coop with consistancy --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 ++++++++++++ .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 55 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..39ebbad842c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb new file mode 100644 index 00000000000..0e70c4e11de --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -0,0 +1,55 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.3'), + ('MUSCLE', '3.8.31'), + ('MAFFT', '7.490', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667-i86linux32', '', True), + ('DIAMOND', '2.0.11'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 415b175f9087a17fe04e76cc8395aaad290dc216 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 18 Dec 2021 20:32:16 +1050 Subject: [PATCH 222/528] dep <- MUSCLE downgrade to coop with consistancy --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 2 +- 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..39ebbad842c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 4309976ceb3..0e70c4e11de 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ ('Seaborn', '0.11.2'), ('FastTree', '2.1.11'), ('IQ-TREE', '2.1.3'), - ('MUSCLE', '5.0.1428', '', True), + ('MUSCLE', '3.8.31'), ('MAFFT', '7.490', '-with-extensions'), ('SEPP', '4.5.0'), ('trimAl', '1.4.1'), From d5f9e39eeb562fc19b6c866718f91973f160a754 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Sat, 18 Dec 2021 20:14:07 +1030 Subject: [PATCH 223/528] Delete PhyloPhlAn-3.0.2-foss-2021a.eb --- .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb deleted file mode 100644 index 0e70c4e11de..00000000000 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ /dev/null @@ -1,55 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v3.0.2 - -easyblock = 'PythonPackage' - -name = 'PhyloPhlAn' -version = '3.0.2' - -homepage = 'https://github.com/biobakery/phylophlan' -description = """ -PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of -genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method -for large-scale microbial genome characterization and phylogenetic analysis -at multiple levels of resolution. -""" - -source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('DendroPy', '4.5.2'), - ('matplotlib', '3.4.2'), - ('Seaborn', '0.11.2'), - ('FastTree', '2.1.11'), - ('IQ-TREE', '2.1.3'), - ('MUSCLE', '3.8.31'), - ('MAFFT', '7.490', '-with-extensions'), - ('SEPP', '4.5.0'), - ('trimAl', '1.4.1'), - ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667-i86linux32', '', True), - ('DIAMOND', '2.0.11'), -] - -use_pip = True -download_dep_fail = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], - 'dirs': ['lib'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -options = {'modulename': '%(namelower)s'} - -moduleclass = 'bio' From e5c00ec28ae6cc8e6b90d4b818e99cf071448513 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Sat, 18 Dec 2021 20:14:21 +1030 Subject: [PATCH 224/528] Delete MUSCLE-3.8.31-GCCcore-10.3.0.eb --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb deleted file mode 100644 index 39ebbad842c..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = '3.8.31' - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] -sources = ['%(namelower)s%(version)s_src.tar.gz'] -patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] -checksums = [ - '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz - '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch -] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -files_to_copy = [ - (["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/muscle"], - 'dirs': [], -} - -moduleclass = 'bio' From 9cab367813c725c6c8c25fef298b811b47c5d6b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 13:57:42 +0100 Subject: [PATCH 225/528] drop unneeded binutils build dep + clarify why full toolchain is used in dlib easyconfigs --- .../easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 4 ++-- easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index 95635f71e04..e62049c61b8 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,8 @@ problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.""" -toolchain = {'name': 'foss', 'version': '2021a'} # requires blas +# dlib can use BLAS/LAPACK, so using full toolchain +toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} github_account = 'davisking' @@ -20,7 +21,6 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb index b3c3383dcf6..8db3464183c 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb @@ -10,6 +10,7 @@ problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.""" +# dlib can use BLAS/LAPACK, so using full toolchain toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'davisking' @@ -18,7 +19,6 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ] From db520140446592c1a815c9e82daee88c46e3df9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 14:22:20 +0100 Subject: [PATCH 226/528] tweak patch for OpenFace + remove unneeded binutils build dep and -DCMAKE_BUILD_TYPE=RELEASE --- .../OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 7 ++---- .../o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 7 ++---- ...Face-2.2.0_avoid-hardcoded-OpenBLAS.patch} | 25 ++++++++++++------- 3 files changed, 20 insertions(+), 19 deletions(-) rename easybuild/easyconfigs/o/OpenFace/{OpenFace-2.2.0-use_FlexiBLAS.patch => OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch} (52%) diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index ffd3307a288..b7b2f6058eb 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -14,14 +14,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'TadasBaltrusaitis' source_urls = [GITHUB_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +patches = ['OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch'] checksums = [ '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz - '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch + 'de366e8af6ffe639b2bf411032e768ba926800389472bb57bb132744c36077b6', # OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch ] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ('patchelf', '0.12') @@ -35,8 +34,6 @@ dependencies = [ ('Boost', '1.76.0'), ] -configopts = "-DCMAKE_BUILD_TYPE=RELEASE" - # This is the only way I found to remove the banned OpenBLAS from libraries # required by the OpenFace executables, as CMake stubbornly includes it there preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb index 9f269dc9eb2..c741d884cad 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -13,14 +13,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'TadasBaltrusaitis' source_urls = [GITHUB_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +patches = ['OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch'] checksums = [ '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz - '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch + 'de366e8af6ffe639b2bf411032e768ba926800389472bb57bb132744c36077b6', # OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch ] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ('patchelf', '0.12') @@ -32,8 +31,6 @@ dependencies = [ ('Boost', '1.76.0'), ] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' - # This is the only way I found to remove the banned OpenBLAS from libraries # required by the OpenFace executables, as CMake stubbornly includes it there preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch similarity index 52% rename from easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch rename to easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch index 105de6d5362..f10fb9becfd 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch @@ -1,6 +1,8 @@ -diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt ---- ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt 2019-07-13 20:20:17.000000000 +0200 -+++ ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt 2021-12-13 23:43:45.160326152 +0100 +replace hardcoding of OpenBLAS to allow use of other BLAS library like FlexiBLAS + +author: Jakub Zárybnický (Inuits) +--- OpenFace-OpenFace_2.2.0/CMakeLists.txt.orig 2021-12-18 14:00:40.813909912 +0100 ++++ OpenFace-OpenFace_2.2.0/CMakeLists.txt 2021-12-18 14:07:55.707025240 +0100 @@ -11,22 +11,19 @@ set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_CONFIG_DIR}") add_definitions(-DCONFIG_DIR="${CONFIG_DIR}") @@ -9,23 +11,28 @@ diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2 -# implementations; so OpenFace wants OpenBLAS; -find_package(OpenBLAS REQUIRED) -if ( ${OpenBLAS_FOUND} ) +- MESSAGE("OpenBLAS information:") +- MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") +-else() +- MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") +if ( DEFINED ENV{LIBBLAS} ) + SET(OpenBLAS_LIB "-L$ENV{BLAS_LIB_DIR} $ENV{LIBBLAS}") - MESSAGE("OpenBLAS information:") - MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") - else() - MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") ++ MESSAGE("BLAS information:") ++ MESSAGE(" BLAS_LIBRARIES: ${OpenBLAS_LIB}") ++ else() ++ MESSAGE(FATAL_ERROR "BLAS not found in the system via \${LIBBLAS}.") endif() -if ( ${OpenBLAS_INCLUDE_FOUND} ) +- MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") +if ( DEFINED ENV{BLAS_INC_DIR} ) + SET(OpenBLAS_INCLUDE_DIR $ENV{BLAS_INC_DIR}) - MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") ++ MESSAGE(" BLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") else() - MESSAGE(WARNING "OpenBLAS include not found in the system. Using the one vended with OpenFace.") - set(OpenBLAS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/lib/3rdParty/OpenBLAS/include") - MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") -+ MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") ++ MESSAGE(FATAL_ERROR "BLAS include dir not found in the system via \${BLAS_INC_DIR}.") endif() find_package( OpenCV 4.0 REQUIRED COMPONENTS core imgproc calib3d highgui objdetect) From 84bc9f307a71f310c92a1cfb577ae95f0a209d7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 15:20:54 +0100 Subject: [PATCH 227/528] use 'readelf -l' to determine path to interpreter in patch file for Rust --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 2 +- .../r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch | 6 +++--- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 1de0bc61268..d9802f22e00 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index ec7ed7d0232..ee8b6cb18e5 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch index 058dc409569..bec629b9175 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch @@ -16,9 +16,9 @@ author: Kenneth Hoste (HPC-UGent) + sysroot = os.getenv("EASYBUILD_SYSROOT") + if sysroot and not fname.endswith(".so"): + # determine patch to interpreter in host via output produced by 'file -b /bin/bash' -+ file_b_out = subprocess.check_output(['file', '-b', '/bin/bash']).decode('ascii', 'ignore').strip() -+ regex = re.compile('.*, interpreter ([^,]*),.*') -+ res = regex.match(file_b_out) ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) + interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) + if not os.path.exists(interpreter_path): + raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index 5e8146115eb..603a5387f6c 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ 'ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976', # rustc-1.54.0-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ From fed954d7f9b2c7310351daf011f7069dbd467d01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 17:19:38 +0100 Subject: [PATCH 228/528] enhance sanity check for PyTorch 1.10.0 with fosscuda/2020b --- .../p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index af85117afc4..a7ff2a282f4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -114,7 +114,13 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' -sanity_check_commands = ["python -c 'import caffe2.python'"] +# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 +# is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "python -c 'import caffe2.python'", + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From 96d985c6a84a5a02e5eaae852c83af843f349d2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 20:09:21 +0100 Subject: [PATCH 229/528] add proper OpenSSL dependency for mold --- easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb index 1b0b1af41f3..d5203935c90 100644 --- a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -19,6 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), ] skipsteps = ['configure'] From 65c2ab143a55ce0cd15641885aa0ff4ebfb3f418 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 19 Dec 2021 00:52:26 +0100 Subject: [PATCH 230/528] disable ccache in MUSCLE v5.0.1428 --- .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb index 17d9c5626cd..e597d772ba5 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb @@ -23,13 +23,13 @@ checksums = [ builddependencies = [ ('binutils', '2.36.1'), - ('ccache', '4.2.1', '', True), ] start_dir = 'src' # Use build environment defined by EB prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" files_to_copy = [(['o/muscle5'], 'bin')] postinstallcmds = ["cd %(installdir)s/bin && ln -s muscle5 muscle"] From 912e0b8f8fc574fa83ff812ceb8889b946016596 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 10:47:56 +0100 Subject: [PATCH 231/528] specify compiler to use in WildMagic easyconfig --- easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb index a7dc62e1381..22c69f44820 100644 --- a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb @@ -17,7 +17,7 @@ dependencies = [ ('freeglut', '3.0.0'), ] -buildopts = "CFG=ReleaseDynamic -f makefile.wm5" +buildopts = 'CFG=ReleaseDynamic -f makefile.wm5 CC="$CXX"' files_to_copy = [ (['SDK/Library/ReleaseDynamic/*'], 'lib'), From 5e9c4b417ba4a01fc24d5ea4f9fc1bc60c2713a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 11:36:03 +0100 Subject: [PATCH 232/528] adding easyconfigs: mold-1.0.0-GCCcore-11.2.0.eb --- .../m/mold/mold-1.0.0-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..98e1d3c8a65 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '1.0.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d7cf170b57a3767d944c80c7468215fa9f8fa176f94f411a5b62b3f56cf07400'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('xxHash', '0.8.0'), + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +skipsteps = ['configure'] + +# PREFIX must be specified when building, to ensure that the mold binary looks for mold-wrapper.so in the right place +buildopts = "PREFIX=%(installdir)s" +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 4d0d3e2a7de94f376782df41afaa0cb33e861f18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 18:04:28 +0100 Subject: [PATCH 233/528] adding easyconfigs: Austin-3.2.0.eb --- .../easyconfigs/a/Austin/Austin-3.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb new file mode 100644 index 00000000000..bbc6c350110 --- /dev/null +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Austin' +version = '3.2.0' + +homepage = 'https://github.com/P403n1x87/austin' +description = "Austin is a Python frame stack sampler for CPython written in pure C." + +toolchain = SYSTEM + +source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] + +cmds_map = [('.*', "$CC -std=c99 -O3 -Os -Wall -pthread src/*.c -o src/austin")] + +files_to_copy = [ + (['src/austin'], 'bin'), + (['src/austin.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/austin', 'share/man/man1/austin.1'], + 'dirs': [], +} + +sanity_check_commands = [ + "austin --help", +] + +moduleclass = 'perf' From a22cf0190aaaecaf2ce42232708743788d0006eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 18:04:53 +0100 Subject: [PATCH 234/528] adding easyconfigs: Austin-3.2.0-GCCcore-11.2.0.eb --- .../a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d4f3285a8fd --- /dev/null +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Austin' +version = '3.2.0' + +homepage = 'https://github.com/P403n1x87/austin' +description = "Austin is a Python frame stack sampler for CPython written in pure C." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] +dependencies = [ + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('protobuf-python', '3.17.3'), +] + +preconfigopts = "autoreconf --install && automake --add-missing && " + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('importlib_resources', '2.0.1', { + 'checksums': ['f5edfcece1cc9435d0979c19e08739521f4cf1aa1adaf6e571f732df6f568962'], + }), + ('austin-python', '1.2.1', { + 'modulename': 'austin', + 'checksums': ['42ba109c031c8c004c348fbbe5c18f177761d3dc531917420de51fa77cdb1fab'], + }), + ('austin-tui', '1.1.0', { + 'checksums': ['b2145a0e1da5095281974e2a37b4e67ce198f5281b7ac48e2801dbf879f46661'], + }), +] + +sanity_check_paths = { + 'files': ['bin/austin', 'bin/austin-tui', 'share/man/man1/austin.1'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "austin --help", + "austin-tui --help", + "pip check", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'perf' From 6ee3bd160c2af1fee5f881fe0cfffc499f56b5be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 23:31:28 +0100 Subject: [PATCH 235/528] stick to minimap2 2.13 as dep for RaGOO + enable download_dep_fail, use_pip, sanity_pip_check --- .../m/minimap2/minimap2-2.17-foss-2018b.eb | 34 ------------------- .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 19 ++++++----- 2 files changed, 11 insertions(+), 42 deletions(-) delete mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb deleted file mode 100644 index 59e42b8bb3f..00000000000 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Adam Huffman -# Big Data Institute, University of Oxford - -easyblock = 'MakeCp' - -name = 'minimap2' -version = "2.17" - -homepage = 'https://github.com/lh3/minimap2' -description = """Minimap2 is a fast sequence mapping and alignment -program that can find overlaps between long noisy reads, or map long -reads or their assemblies to a reference genome optionally with detailed -alignment (i.e. CIGAR). At present, it works efficiently with query -sequences from a few kilobases to ~100 megabases in length at an error -rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited -test data sets, minimap2 is over 20 times faster than most other -long-read aligners. It will replace BWA-MEM for long reads and contig -alignment.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] -sources = ['%(name)s-%(version)s.tar.bz2'] -checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] - -files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb index a76297e3b5a..613e17d4b4d 100644 --- a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'RaGOO' version = '1.11' @@ -19,18 +19,21 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] dependencies = [ - ('Python', '3.6.6'), - ('minimap2', '2.17'), - ('intervaltree', '3.0.2', '-Python-%(pyver)s'), - # numpy dependency is provided by the python module + ('Python', '3.6.6'), # provides numpy + ('minimap2', '2.13'), + ('intervaltree', '3.0.2', versionsuffix), ] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': ['bin/ragoo.py'], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -# workaround for the python sanity check trying to do 'import ragoo' -options = {'modulename': 'os'} +options = {'modulename': 'ragoo_utilities'} + +sanity_pip_check = True moduleclass = 'bio' From e486f98357cc78aac7947e760fc698a077890fe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 23:40:00 +0100 Subject: [PATCH 236/528] add back attribution in dill easyconfig --- easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb index d6147e812d7..68674f3f2c1 100644 --- a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb @@ -1,3 +1,4 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. easyblock = 'PythonPackage' name = 'dill' From 12ef2fe98e0e154660a335062731a8c651d24185 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:07:56 +0100 Subject: [PATCH 237/528] avoid unneeded local variables in Embree easyconfig --- ...Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 8d9da0f977c..c7a26e87bcc 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -1,10 +1,7 @@ easyblock = 'CMakeMake' -name = 'Embree' -version = "3.4.0" -gccver = '6.4.0' -binutilsver = '2.28' -gccsuff = '-GCC-%s' % (gccver) +name = 'Embree' +version = '3.4.0' homepage = 'https://embree.github.io/' description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. @@ -15,7 +12,7 @@ Intel® Embree supports runtime code selection to choose the traversal and build the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" -toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} +toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} source_urls = ['https://github.com/embree/embree/archive/'] sources = ['v%(version)s.tar.gz'] @@ -25,7 +22,7 @@ builddependencies = [('CMake', '3.11.4')] dependencies = [ ('ispc', '1.10.0', '', True), - ('tbb', '2018_U5', '', ('GCCcore', gccver)), + ('tbb', '2018_U5'), ] configopts = '-DEMBREE_TUTORIALS=OFF ' From 8e55025073b285a273ead89fc55ecf1a11dd21b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:17:46 +0100 Subject: [PATCH 238/528] rename intervaltree Python package to intervaltree-python + install it via PythonBundle since it also required sortedcontainers --- ...ee-python-3.0.2-foss-2018b-Python-3.6.6.eb | 41 +++++++++++++++++++ ...ervaltree-3.0.2-foss-2018b-Python-3.6.6.eb | 30 -------------- .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 2 +- 3 files changed, 42 insertions(+), 31 deletions(-) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb delete mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e1cca3746a6 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonBundle' + +name = 'intervaltree-python' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by point, by range overlap, + or by range containment""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', version, { + 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index ca15abe5443..00000000000 --- a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'PythonPackage' - -name = 'intervaltree' -version = '3.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/chaimleib/intervaltree' -description = 'A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment' - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['https://github.com/chaimleib/intervaltree/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['e8ab75b66077f2e5fb85ac56cb6df834689edb048d38601d53d8867cce3b77d1'] - -dependencies = [ - ('Python', '3.6.6'), -] - -sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/intervaltree-%(version)s-py%(pyshortver)s.egg'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb index 613e17d4b4d..939bf3e3e31 100644 --- a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -21,7 +21,7 @@ checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] dependencies = [ ('Python', '3.6.6'), # provides numpy ('minimap2', '2.13'), - ('intervaltree', '3.0.2', versionsuffix), + ('intervaltree-python', '3.0.2', versionsuffix), ] download_dep_fail = True From 365f167295014f011eb25d067c2a8a246709f57a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:24:43 +0100 Subject: [PATCH 239/528] use $CFLAGS rather than hardcoding '-O3 -Os' in Austin easyconfig Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb index bbc6c350110..2ed5b3c23eb 100644 --- a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] -cmds_map = [('.*', "$CC -std=c99 -O3 -Os -Wall -pthread src/*.c -o src/austin")] +cmds_map = [('.*', "$CC $CFLAGS -std=c99 -Wall -pthread src/*.c -o src/austin")] files_to_copy = [ (['src/austin'], 'bin'), From acd4fa055198a9813eed2199806bff878b099e02 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 00:28:01 +0100 Subject: [PATCH 240/528] pass compiler set by EB to build of ExaML v3.0.22 --- .../e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb index 7840f1a156e..8c5ef0fc82c 100644 --- a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -10,6 +10,7 @@ homepage = 'https://github.com/stamatak/ExaML/' description = "Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI" toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} github_account = 'stamatak' source_urls = [GITHUB_SOURCE] @@ -17,7 +18,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] prebuildopts = 'cd examl &&' -buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' +buildopts = '-f Makefile.OMP.AVX.gcc CC="$CC" &&' +buildopts += 'cd ../parser && make -f Makefile.SSE3.gcc CC="$CC"' files_to_copy = [(['examl/examl-OMP-AVX', 'parser/parse-examl'], 'bin'), 'README.md', 'manual'] From d213bf5fb99c49ba1f44eb29cbd667f3fb70e6d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:36:34 +0100 Subject: [PATCH 241/528] add custom sanity_check_paths for Embree --- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index c7a26e87bcc..328732419a3 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -27,4 +27,9 @@ dependencies = [ configopts = '-DEMBREE_TUTORIALS=OFF ' +sanity_check_paths = { + 'files': ['lib/libembree3.%s' % SHLIB_EXT], + 'dirs': ['bin/embree3/models', 'include/embree3', 'lib/cmake/embree-%(version)s', 'share'], +} + moduleclass = 'vis' From 359c72b4cd816d2971683088a0fe7b1b77f1f94b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:44:06 +0100 Subject: [PATCH 242/528] explain why h5py v2.10.0 is bundled in yaff-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index 229465a24ee..03214bbd476 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -34,6 +34,7 @@ local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/m local_runtest += "python setup.py build_ext -i; nosetests -v" exts_list = [ + # yaff v1.6.0 does not work with h5py>=3.0, the default version in foss/2020b ('h5py', '2.10.0', { 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', From 20683302b5f345da56b32e205c151a1902496f2f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:45:20 +0100 Subject: [PATCH 243/528] remove default sanity checks from molmod v1.4.8 --- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 55945818bbf..1aa8772b2ae 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -26,9 +26,4 @@ sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; pytest -ra" -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' From b43165020bc7df9a7acd1145dacf3de22cd288b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 08:26:35 +0100 Subject: [PATCH 244/528] don't set download_dep_fail in intervaltree-python easyconfig --- .../intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb index e1cca3746a6..c32e4755def 100644 --- a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb @@ -19,7 +19,6 @@ dependencies = [ ('Python', '3.6.6'), ] -download_dep_fail = True use_pip = True exts_list = [ From 68ef107266284e1ec7bd1ea8a231f2351e4f15e9 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:27:47 +0200 Subject: [PATCH 245/528] adding easyconfigs: MultiQC-1.11-foss-2021a.eb --- .../m/MultiQC/MultiQC-1.11-foss-2021a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb new file mode 100644 index 00000000000..0c12b69d6ad --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.11' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), + ('PyYAML', '5.4.1'), + ('networkx', '2.6.3'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['6633ec44d8aed5477283158c613a46d27d3581d41baf0ecfac451a914870bab6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 045f3d0a5a89071e9401b1e87334f11eff174ccb Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:28:32 +0200 Subject: [PATCH 246/528] adding easyconfigs: MultiQC-1.10.1-foss-2020b.eb --- .../m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb new file mode 100644 index 00000000000..c89209dad06 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.10.1' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('networkx', '2.5'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['a4be38dd72da6b3b042d5dffbdcafd3e368189fbc4e767c79ce0aea1987c3a79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 07af3b65149806bea88810beaf1bcf1344cc182f Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:56:09 +0200 Subject: [PATCH 247/528] using networkx=2.5.1 --- easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb index 0c12b69d6ad..0601bdf5eba 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.5'), ('matplotlib', '3.4.2'), ('PyYAML', '5.4.1'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] use_pip = True From fe8365ebf123082d8fe29212db2cc0cf72d49972 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 15:56:46 +0100 Subject: [PATCH 248/528] Update easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit added info comments Co-authored-by: Bob Dröge --- .../easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb index c89209dad06..ef76f02541b 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' From 4f69f2896cdcbd107d0f3eecd095064efeac79e8 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 15:58:47 +0100 Subject: [PATCH 249/528] Update easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit added info comments Co-authored-by: Bob Dröge --- .../easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb index 0601bdf5eba..f6a7cc770c2 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' From 12a01f35087866a8213007f0a0e7c2190ebb8ec8 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 16:39:41 +1050 Subject: [PATCH 250/528] dep <- name change fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index bca8f6f7144..1181824b3f9 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -40,7 +40,7 @@ dependencies = [ ('minimap2', '2.20'), ('Mash', '2.3'), ('cDNA_Cupcake', '26.0.0'), - ('python-pulp', '2.5.1'), + ('PuLP', '2.5.1'), ] download_dep_fail = True From 7e6c5ecc9e397307eb6da295073ecb202c7aef95 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 17:00:39 +1050 Subject: [PATCH 251/528] dep <- version conflict fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 1181824b3f9..1dd3d1104e6 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('scikit-image', '0.18.3'), ('Biopython', '1.79'), ('bx-python', '0.8.11'), From 98110f1bfa4a795e6f83335b297f98aae606d228 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 17:13:55 +1050 Subject: [PATCH 252/528] debug <- style fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 1dd3d1104e6..4c4c6c07fcc 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -50,8 +50,7 @@ sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['run_mash.py', 'process_kmer_to_graph.py', - 'reconstruct_contig.py'] - ], + 'reconstruct_contig.py']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 81f38bf117b5baf40a42861843f843634ef9c173 Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Tue, 21 Dec 2021 08:43:32 +0100 Subject: [PATCH 253/528] Julia LTS update v1.6.5 --- .../j/Julia/Julia-1.6.5-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb new file mode 100644 index 00000000000..9488e9084d1 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.5' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 6ed38d6da0e1e083216d2d2ae019b1de28225db7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Dec 2021 09:18:26 +0100 Subject: [PATCH 254/528] remove FastTree easyconfig, merged in #14564 --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb deleted file mode 100644 index e210cab5b2b..00000000000 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'CmdCp' - -name = 'FastTree' -version = '2.1.11' - -homepage = 'https://www.microbesonline.org/fasttree/' -description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide - or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of - time and memory. """ - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.microbesonline.org/fasttree/'] -sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] -checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] - -builddependencies = [('binutils', '2.36.1')] - -cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] - -files_to_copy = [(['FastTree'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/FastTree'], - 'dirs': [], -} - -sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] - -moduleclass = 'bio' From 8a18edfea8ab88a51443fb3fa8eae29aa9e1dd7a Mon Sep 17 00:00:00 2001 From: Max Voit Date: Tue, 21 Dec 2021 12:03:15 +0100 Subject: [PATCH 255/528] adding easyconfigs: CAFE5-5.0.0-GCC-10.2.0.eb --- .../c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..e1a52c7d446 --- /dev/null +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'CAFE5' +version = '5.0.0' + +homepage = 'https://github.com/hahnlab/CAFE5' + +description = """Software for Computational Analysis of gene Family Evolution + +The purpose of CAFE is to analyze changes in gene family size in a way that +accounts for phylogenetic history and provides a statistical foundation for +evolutionary inferences. The program uses a birth and death process to model +gene gain and loss across a user-specified phylogenetic tree. The distribution +of family sizes generated under this model can provide a basis for assessing the +significance of the observed family size differences among taxa. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +#toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +builddependencies = [] + +dependencies = [] + +install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/cafe5', + ], + 'dirs': ['bin', 'examples'], +} + +moduleclass = 'bio' From 566fa5ff37689878f98dde75979fc4fd0a65ce22 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 12:06:28 +0100 Subject: [PATCH 256/528] Update CAFE5-5.0.0-GCC-10.2.0.eb --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index e1a52c7d446..8b45dda0bc2 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,5 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# Author: Max Voit easyblock = 'ConfigureMake' From 72b4b183def9cc5f6dd77e22a36c3db1fad233ea Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:50:54 +0100 Subject: [PATCH 257/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 8b45dda0bc2..63828151ad0 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -15,8 +15,7 @@ accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the -significance of the observed family size differences among taxa. -""" +significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} From b881ae31d219f831a23311e6ac08d53a8ba9addc Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:06 +0100 Subject: [PATCH 258/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 63828151ad0..3c49fe65082 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] builddependencies = [] From 243125a8de9ccae1ce636ff5ee1abdb12c44eb27 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:14 +0100 Subject: [PATCH 259/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 3c49fe65082..1e837f985a4 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,11 +23,6 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] - -builddependencies = [] - -dependencies = [] - install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From c3aea9dfe19884e970e827acec4e99c52fea1226 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:19 +0100 Subject: [PATCH 260/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 1e837f985a4..a631bd275a2 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -26,8 +26,7 @@ checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { - 'files': ['bin/cafe5', - ], + 'files': ['bin/cafe5'], 'dirs': ['bin', 'examples'], } From 337dd3673aa4bc1195aa6f1cdef38c0e6889fe13 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:27 +0100 Subject: [PATCH 261/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index a631bd275a2..efbb78a6685 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -30,4 +30,6 @@ sanity_check_paths = { 'dirs': ['bin', 'examples'], } +sanity_check_commands = ['cafe5 --help'] + moduleclass = 'bio' From 2878927820030073dd2f4f39af9c2e9ae10379be Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:48:59 +0100 Subject: [PATCH 262/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index efbb78a6685..01a1de16141 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -27,7 +27,7 @@ install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 sanity_check_paths = { 'files': ['bin/cafe5'], - 'dirs': ['bin', 'examples'], + 'dirs': ['examples'], } sanity_check_commands = ['cafe5 --help'] From eb7d1e781851b627aed1c522f2ad7b922651cf0b Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:05 +0100 Subject: [PATCH 263/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 01a1de16141..9b18ee21156 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,6 +23,8 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From 56ef3a1d4dbfac337e3dbb8c5841043e6a0c0632 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:12 +0100 Subject: [PATCH 264/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9b18ee21156..9706d2a7224 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -18,7 +18,7 @@ of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -#toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] From 62a15974a958a112d6c5035935f0c5d822815ae2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Dec 2021 16:51:03 +0100 Subject: [PATCH 265/528] add ICU dependency for Qt5 v5.15.2 Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 2d43727ea14..18e55bea4a7 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -60,6 +60,7 @@ dependencies = [ ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', True), + ('ICU', '69.1'), ] # qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) From 05533f8c94720a038fcfc95c048043b414e94893 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 16:54:20 +0000 Subject: [PATCH 266/528] Add git as build dependency. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb index 9495f86059e..3a04eb5df1c 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Yasm', '1.3.0'), + ('git', '2.32.0', '-nodocs'), ] start_dir = 'source' From 85cdfe87241377a9658b40a75eb83a26b4def7cc Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 17:26:11 +0000 Subject: [PATCH 267/528] Remove git dependency, force check to assume it's a downloaded archive. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb index 3a04eb5df1c..e4954e8ef8c 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb @@ -21,11 +21,12 @@ builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Yasm', '1.3.0'), - ('git', '2.32.0', '-nodocs'), ] start_dir = 'source' +configopts = '-DGIT_ARCHETYPE=1' + sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], 'dirs': [], From dc26caecb680cf4f559c53e4e602457eb666d81e Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 18:09:19 +0000 Subject: [PATCH 268/528] Added fix to x265-3.5-GCCcore-11.2.0.eb. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb index 8b337e94692..0732a992f17 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb @@ -25,6 +25,8 @@ builddependencies = [ start_dir = 'source' +configopts = '-DGIT_ARCHETYPE=1' + sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], 'dirs': [], From 1f94d739cb7dd1971abcf7a59897348ac1b0ccad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Dec 2021 21:00:38 +0100 Subject: [PATCH 269/528] adding easyconfigs: gnuplot-5.4.2-GCCcore-11.2.0.eb, libgd-2.3.3-GCCcore-11.2.0.eb --- .../g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb | 35 +++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c2af06feb4c --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.2' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('libgd', '2.3.3'), + ('Pango', '1.48.8'), + ('libcerf', '1.17'), + ('X11', '20210802'), + ('Qt5', '5.15.2'), + ('Lua', '5.4.3'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..30b7642af4e --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('fontconfig', '2.13.94'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' From 3f311319f8b9a0632093d312cb43fd5ba4ce51b3 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 22 Dec 2021 10:04:45 +0100 Subject: [PATCH 270/528] adding easyconfigs: gmsh-4.9.0-foss-2021a-Python-3.9.5.eb, occt-7.5.0p1-foss-2021a.eb, FreeImage-3.18.0-GCCcore-10.3.0.eb --- .../FreeImage-3.18.0-GCCcore-10.3.0.eb | 39 ++++++++++++++++ .../gmsh-4.9.0-foss-2021a-Python-3.9.5.eb | 43 ++++++++++++++++++ .../o/occt/occt-7.5.0p1-foss-2021a.eb | 45 +++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6791fe420e5 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] +installopts = [ + 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', + '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..0a2c21fd5ee --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gmsh.info/' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {"usempi": True} + +source_urls = ['https://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['b8ef133c9b66ffe12df1747e72d4acf19f1eb1e9cd95eb0f577cbc4081d9bea3'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('PETSc', '3.15.1'), + ('SLEPc', '3.15.1'), + ('FLTK', '1.3.6'), + ('occt', '7.5.0p1'), +] + +separate_build_dir = True + +configopts = '-DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib64']} + +sanity_check_paths = { + 'files': ['bin/gmsh', 'bin/onelab.py'], + 'dirs': [], +} + +sanity_check_commands = ["gmsh --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb new file mode 100644 index 00000000000..f9d90b33602 --- /dev/null +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'occt' +version = '7.5.0p1' + +homepage = 'https://www.opencascade.com/' +description = """Open CASCADE Technology (OCCT) is an object-oriented C++ +class library designed for rapid production of sophisticated domain-specific +CAD/CAM/CAE applications.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.salome-platform.org/Salome/other'] +sources = ['opencascade-%(version)s.tar.gz'] +checksums = ['c0bbe42f0c41b6dcd6a39a83961ca7e414eb2d5d919f4dcb930096f2a423a578'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('freetype', '2.10.4'), + ('Tcl', '8.6.11'), + ('Tk', '8.6.11'), + ('FreeImage', '3.18.0'), + ('tbb', '2020.3'), +] + +separate_build_dir = True + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " +configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " +configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " +configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " +configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " + +sanity_check_paths = { + 'files': ['bin/DRAWEXE', 'bin/env.sh'], + 'dirs': ['lib/cmake/opencascade'], +} + +moduleclass = 'cae' From 8d719b09fa0eeae7c680b049d11c33a988125a5f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 22 Dec 2021 09:19:23 +0000 Subject: [PATCH 271/528] adding easyconfigs: numdiff-5.9.0-GCCcore-10.2.0.eb --- .../n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9c49693bbc4 --- /dev/null +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numdiff' +version = '5.9.0' + +homepage = 'https://savannah.nongnu.org/projects/numdiff' +description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. + Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields + (and not only).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['87284a117944723eebbf077f857a0a114d818f8b5b54d289d59e73581194f5ef'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/ndselect', 'bin/numdiff'], + 'dirs': ['share'], +} + +sanity_check_commands = ["numdiff --help"] + +moduleclass = 'tools' From 8f9b57573dcd7b2c9b09e3c5f32505358c58f4b5 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 22 Dec 2021 09:36:16 +0000 Subject: [PATCH 272/528] switch homepage MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb index 9c49693bbc4..b8f9bfcd13d 100644 --- a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'numdiff' version = '5.9.0' -homepage = 'https://savannah.nongnu.org/projects/numdiff' +homepage = 'https://www.nongnu.org/numdiff/' description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields From a1827ca68d6470cb353d46814f251a5d3c3719b0 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 22 Dec 2021 11:56:44 +0100 Subject: [PATCH 273/528] Removed versionsuffix --- ...4.9.0-foss-2021a-Python-3.9.5.eb => gmsh-4.9.0-foss-2021a.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/g/gmsh/{gmsh-4.9.0-foss-2021a-Python-3.9.5.eb => gmsh-4.9.0-foss-2021a.eb} (96%) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb similarity index 96% rename from easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb index 0a2c21fd5ee..dbc13d8c38f 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'gmsh' version = '4.9.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" From 0504cf0668d1c7ca233ec6ef571213a21e54c121 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 22 Dec 2021 12:15:38 +0100 Subject: [PATCH 274/528] adding easyconfigs: JUBE-2.4.2.eb --- easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb | 31 ++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb new file mode 100644 index 00000000000..7fe48f84a3e --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb @@ -0,0 +1,31 @@ +easyblock = "VersionIndependentPythonPackage" + +name = "JUBE" +version = "2.4.2" + +homepage = "https://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based +framework to easily create benchmark sets, run those sets on different +computer systems and evaluate the results. +""" + +toolchain = SYSTEM + +source_urls = ['https://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['d1de15e9792802f83521b582d1d144ec81e3d5a28c01dbd945288ea29b946729'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [], +} + +modextrapaths = { + 'JUBE_INCLUDE_PATH': 'share/jube/platform/slurm' +} + +modluafooter = 'execute {cmd=\'eval "$(jube complete)"\',modeA={"load"}}' + +moduleclass = 'tools' From c04db4bf3671a1d5060ac426b9f5a7171f138892 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 12:36:22 +0100 Subject: [PATCH 275/528] add 'webpng --help' as sanity check command for libgd MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb index 30b7642af4e..f483ddfc597 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include'], } +sanity_check_commands = ['webpng --help'] + moduleclass = 'lib' From 51fe4983134e9d445fd56ff620b0cc1fbf061b79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 13:40:05 +0100 Subject: [PATCH 276/528] remove commented out license_file spec in itac 2021.2.0 easyconfig --- easybuild/easyconfigs/i/itac/itac-2021.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index b95225dd483..3deaaa9e711 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -19,7 +19,4 @@ dontcreateinstalldir = True preferredmpi = 'impi5' -# license file -# license_file = HOME + '/licenses/intel/license.lic' - moduleclass = 'tools' From 389bcf7aadc1379c08f9d557dff5571abaf1f929 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 22 Dec 2021 14:20:34 +0100 Subject: [PATCH 277/528] Add sanity check command for occt --- easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb index f9d90b33602..7c0a089a242 100644 --- a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { 'dirs': ['lib/cmake/opencascade'], } +sanity_check_commands = ['DRAWEXE -h'] + moduleclass = 'cae' From 429c3a3d372721a05c34f0ee2229551f1d9c4235 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 15:05:04 +0100 Subject: [PATCH 278/528] stick to libunwind 1.4.0 as dependency for Extra 3.8.3 with gompi/2021a --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index a58b66ffa82..d10c82b4856 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -24,7 +24,7 @@ checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] dependencies = [ ('zlib', '1.2.11'), ('Boost', '1.76.0'), - ('libunwind', '1.5.0'), + ('libunwind', '1.4.0'), ('libxml2', '2.9.10'), ('libdwarf', '20210305'), ('PAPI', '6.0.0.1'), From ddd8b575d79467eb12b3ca009e65e486ed8921da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 16:13:50 +0100 Subject: [PATCH 279/528] add sanity check command for libdwarf 20210305 --- .../easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb index 4d501a86e34..e2175d20e81 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['include'] } +sanity_check_commands = ['dwarfdump --help'] + moduleclass = 'devel' From 7ac359f1a2ee8cfd1c69d116d59ad9877e1ab2e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 16:15:26 +0100 Subject: [PATCH 280/528] fix checksum for Extrae 3.8.3 --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index d10c82b4856..4662280bbb5 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] -checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] +checksums = ['1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198'] dependencies = [ ('zlib', '1.2.11'), From ee268254bf06dcee65a9631653b2d334007dd253 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 18:04:00 +0100 Subject: [PATCH 281/528] accept both original and current checksum for source tarball of Extrae 3.8.3 --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index 4662280bbb5..f1082fc78ce 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -19,7 +19,8 @@ toolchainopts = {'usempi': True} source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] -checksums = ['1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198'] +checksums = [('32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b', + '1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198')] dependencies = [ ('zlib', '1.2.11'), From bc7530a9fe980d7ff9befdb9a1f18db1394af6ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 22 Dec 2021 18:25:49 +0100 Subject: [PATCH 282/528] add simple sanity check for jube --- easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb index 7fe48f84a3e..8a1b74a328a 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb @@ -22,6 +22,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jube --version'] + modextrapaths = { 'JUBE_INCLUDE_PATH': 'share/jube/platform/slurm' } From ba8eb244b26fa44b344ec4f15f0e13de3a1b74b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 20:44:58 +0100 Subject: [PATCH 283/528] enable sanity_pip_check in Calcam easyconfigs --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 7 ++++--- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index ba8db2d6ade..aa81fc28ef0 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -27,9 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] -use_pip = True - download_dep_fail = True +use_pip = True # Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. # The following line answers "n" to this question and skips the conversion. @@ -37,7 +36,9 @@ preinstallopts = 'echo n |' sanity_check_paths = { 'files': ['bin/calcam'], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 193dc5501b8..14e871b7aee 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -27,9 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] -use_pip = True - download_dep_fail = True +use_pip = True # Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. # The following line answers "n" to this question and skips the conversion. @@ -37,7 +36,9 @@ preinstallopts = 'echo n |' sanity_check_paths = { 'files': ['bin/calcam'], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'phys' From 0f0bbe94b15ebc5373adb15814891c8a1bacc344 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 22:36:08 +0100 Subject: [PATCH 284/528] add missing preinstallopts + strip out unneeded source_urls in easyconfig for numba 0.50.1 --- .../n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index e5b096d734b..b6e4f5a3a9d 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ sanity_pip_check = True exts_list = [ ('llvmlite', '0.33.0', { 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", 'checksums': [ '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', # llvmlite-0.33.0.tar.gz # llvmlite-0.30.0_fix-ffi-Makefile.patch @@ -34,7 +34,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7'], }), ] From 207c0002aaff2de51a9d07eafb6b13d2e3009be8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:12 +0100 Subject: [PATCH 285/528] add patch to fix build of Arrow 0.17.1 on aarch64 systems + fix configure options --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e4c0d64a274..e348b0044cb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -9,15 +9,12 @@ description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'http://apache.belnet.be/arrow/arrow-%(version)s/', - 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', -] +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-0.16.0_fix-intel.patch'] +patches = ['Arrow-0.17.1_fix-arm.patch'] checksums = [ 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz - '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch + 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch ] builddependencies = [ @@ -35,18 +32,18 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] From d2a00a14ad6d00cd83dff4ec75defd3183c9631f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:28 +0100 Subject: [PATCH 286/528] add archive source URL for Spark 3.1.1 --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index ba34f767b68..5cb1ec3c5ee 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -11,6 +11,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] @@ -25,13 +26,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] From b642e2b4c3ce9a9850a6c68954ad9a7e46a854ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:26:30 +0100 Subject: [PATCH 287/528] adding easyconfigs: DyMat-0.7-foss-2021b-2020-12-12.eb --- .../DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb diff --git a/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb b/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb new file mode 100644 index 00000000000..f7de7bbb8f3 --- /dev/null +++ b/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'DyMat' +version = '0.7' +local_commit = '3ce988f' +versionsuffix = '-2020-12-12' + +homepage = 'https://www.j-raedler.de/projects/DyMat' +description = "Read and process result files from Dymola and OpenModelica with Python." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/jraedler/DyMat/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'DyMat-%(version)s%(versionsuffix)s.tar.gz'}] +checksums = ['57ea1ac7c28aeb6fce1e3efdc7a5b11ee54ac015643453bff6b5996594bf84d2'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/DyMatExport.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cd %(builddir)s/DyMat-*/test && python Test.py", + "cd %(builddir)s/DyMat-*/test && DyMatExport.py --info DoublePendulum_Dymola-2012.mat", +] + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'tools' From 45ab6ccc84104ad8090736ae625d74151941265e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:41:18 +0100 Subject: [PATCH 288/528] adding easyconfigs: PyCalib-0.1.0.dev0-foss-2021b.eb --- .../PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb b/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb new file mode 100644 index 00000000000..0782d64ca15 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyCalib' +version = '0.1.0.dev0' + +homepage = 'https://github.com/classifier-calibration/PyCalib' +description = "Python library for classifier calibration" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6f9662e5219d85aed5b91c0cd391e2297c9b94229c7591796a84f5e6f742168b'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('statsmodels', '0.13.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 5b078e635f33e802aea7c024d07feaecf2442d3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:59:53 +0100 Subject: [PATCH 289/528] adding easyconfigs: alevin-fry-0.4.3-GCCcore-11.2.0.eb --- .../alevin-fry-0.4.3-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9fcc9fd98d1 --- /dev/null +++ b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'alevin-fry' +version = '0.4.3' + +homepage = 'https://github.com/COMBINE-lab/alevin-fry' +description = """alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, + currently focused on single-cell transcriptomics and feature barcoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/COMBINE-lab/alevin-fry/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['407a1b5767a293aefa9ff1dc2eda478356e74d148e3bfa89ef58213340e87ae2'] + +builddependencies = [ + ('binutils', '2.37'), + ('Rust', '1.54.0'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +extract_sources = True + +# pin version of clap dependency, +# see https://github.com/COMBINE-lab/alevin-fry/commit/dcdd91cb6ff49065f60f3b6b400bd023fc308ab6 +install_cmd = "sed -i 's/3.0.0-beta.5/=3.0.0-beta.5/g' Cargo.toml && " +install_cmd += "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 20a494ef1dc00c99aa90aebaba235d0c3c182c48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 13:55:18 +0100 Subject: [PATCH 290/528] fix broken patch file for recent GPAW versions --- .../g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch | 2 +- .../easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb | 2 +- .../g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 2 +- .../g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch index e64b4d0f7da..551d7ead70d 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch @@ -24,7 +24,7 @@ new file mode 100644 index 0000000..5be60fa --- /dev/null +++ b/doc/platforms/Linux/EasyBuild/config_foss.py -@@ -0,0 +1,49 @@ +@@ -0,0 +1,53 @@ +# Convert static library specs from EasyBuild to GPAW +def static_eblibs_to_gpawlibs(lib_specs): + return [libfile[3:-2] for libfile in os.getenv(lib_specs).split(',')] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb index 49832a9822a..06c705f51cb 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb index f87fd8a0abd..fc6b25cdb3d 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb index 67379b2bc14..31e4e602dc0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -24,7 +24,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1dd3ad51a45..1b322074614 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb index 784eb04d4fa..7535f24c1a0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -24,7 +24,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 8264ef0a7fd..861a80e2fd1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 77370423b34..7a2e4989e8a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index f8f2758be19..1f22f89cc83 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index f2b603dd335..582e90ea73b 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb index c88a6eea7e1..4abf305f2a6 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bedc11e9043..bba61ad1209 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] # The intel version is not built with libvdwxc support, as that library is incompatible with MKL. From e4b5758f09ccf0d74e707b0e03a8c60aa5fb1f42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 14:28:32 +0100 Subject: [PATCH 291/528] {toolchain} intel/2022.00 --- .../h/HPL/HPL-2.3-intel-2022.00.eb | 21 +++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.00.eb | 18 +++++++++++ .../imkl-FFTW-2022.0.1-iimpi-2022.00.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb | 16 ++++++++++ .../impi-2021.5.0-intel-compilers-2022.0.1.eb | 16 ++++++++++ .../intel-compilers-2022.0.1.eb | 31 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.00.eb | 22 +++++++++++++ 7 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.00.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb new file mode 100644 index 00000000000..fbc0e91b70f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.00'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb new file mode 100644 index 00000000000..715e4a7748a --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.00' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.0.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb new file mode 100644 index 00000000000..2eaf7432065 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.00'} + +dependencies = [('imkl', version, '', True)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb new file mode 100644 index 00000000000..67a5563ac0b --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -0,0 +1,16 @@ +name = 'imkl' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +sources = ['l_onemkl_p_%(version)s.117_offline.sh'] +checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] + +interfaces = False + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb new file mode 100644 index 00000000000..bee00810199 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.5.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] +checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] + +dependencies = [('UCX', '1.11.2')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb new file mode 100644 index 00000000000..56c8e9b5da4 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -0,0 +1,31 @@ +name = 'intel-compilers' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', + }, +] +checksums = [ + 'c7cddc64c3040eece2dcaf48926ba197bb27e5a46588b1d7b3beddcdc379926a', # l_dpcpp-cpp-compiler_p_2022.0.1.71_offline.sh + '2cb28a04f93554bfeffd6cad8bd0e7082735f33d73430655dea86df8933f50d1', # l_fortran-compiler_p_2022.0.1.70_offline.sh +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.00.eb b/easybuild/easyconfigs/i/intel/intel-2022.00.eb new file mode 100644 index 00000000000..756e76c67c6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.00.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.00' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.0.1' +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', True), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 83aa6f4c1b3fca801bd9df250ff4a78c475bff50 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:44:31 +0100 Subject: [PATCH 292/528] adding easyconfigs: Spack-0.17.0.eb --- easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb new file mode 100644 index 00000000000..3d643965035 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Spack' +version = '0.17.0' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/spack/spack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93df99256a892ceefb153d48e2080c01d18e58e27773da2c2a469063d67cb582'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' From 08625042f3dd6c8e215ff922ffe7f860f62f9fba Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:52:59 +0100 Subject: [PATCH 293/528] adding easyconfigs: dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb --- ...otNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..20136cc0efc --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +# note: only works on recent OSs, required sufficiently recent glibc (2.14 or newer) +name = 'dotNET-Core-Runtime' +version = '6.0.1' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'be8a513c-f3bb-4fbd-b382-6596cf0d67b5/968e205c44eabd205b8ea98be250b880'] +sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] +checksums = ['f77369477ee8c98402793a2b6ce1f46d663fd0373a93a4cef50eb22d8607773c'] + +dependencies = [('libunwind', '1.5.0')] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], +} + +modextrapaths = {'PATH': ['']} + +moduleclass = 'lang' From 5d4c06a94a352fc96c7ae1a34f74433fe94d6fc8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:54:54 +0100 Subject: [PATCH 294/528] adding easyconfigs: dotNET-SDK-6.0.101-linux-x64.eb --- .../dotNET-SDK-6.0.101-linux-x64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb new file mode 100644 index 00000000000..7e1702a66c2 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -0,0 +1,31 @@ +## +# Authors:: Robert Qiao +# Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'dotNET-SDK' +version = '6.0.101' +versionsuffix = '-linux-x64' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = SYSTEM +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'ede8a287-3d61-4988-a356-32ff9129079e/bdb47b6b510ed0c4f0b132f7f4ad9d5a'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['95a1b5360b234e926f12327d68c4a0d7b7206134dca1b570a66dc7a8a4aed705'] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], +} + +modextrapaths = { + 'PATH': [''], + 'DOTNET_ROOT': [''], +} + +moduleclass = 'lang' From 50fe9b8001d4a62ece2578392e458cea3ed5cfbe Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:06:25 +0100 Subject: [PATCH 295/528] adding easyconfigs: AMD-uProf-3.4.502.eb --- .../a/AMD-uProf/AMD-uProf-3.4.502.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb new file mode 100644 index 00000000000..37ec97a3ea8 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Binary' + +name = 'AMD-uProf' +version = '3.4.502' + +homepage = 'https://developer.amd.com/amd-uprof/' +description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.amd.com/wordpress/media/files/'] +sources = ['AMDuProf_Linux_x64_%(version)s.tar.bz2'] +checksums = ['891463c0e4f20e1c67a145441e983c863156a52716234cd8d5a96a8d09635ba7'] + +extract_sources = True + +sanity_check_paths = { + 'files': ['include/AMDTPowerProfileApi.h', 'lib/x64/libAMDProfileController.a', + 'bin/libAMDThreadProfileAPI.%s' % SHLIB_EXT, 'bin/AMDuProf'], + 'dirs': ['Examples'] +} + +sanity_check_commands = ['AMDuProfCLI info --system'] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'bin' +} + +moduleclass = 'perf' From 52b2658de66447e2c4960bee6959435e688f2d42 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:10:17 +0100 Subject: [PATCH 296/528] adding easyconfigs: VTune-2022.0.0.eb --- .../easyconfigs/v/VTune/VTune-2022.0.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb new file mode 100644 index 00000000000..e205471e1e5 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2022.0.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] +checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From b1cd41425aae067643e33c45d60adea3a8a2e07d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:13:40 +0100 Subject: [PATCH 297/528] adding easyconfigs: itac-2021.5.0.eb --- easybuild/easyconfigs/i/itac/itac-2021.5.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.5.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb new file mode 100644 index 00000000000..f9d10379c85 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'itac' +version = '2021.5.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] +checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +moduleclass = 'tools' From 6190404ea12fd371138b2997d730227d51eb8c35 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:14:53 +0100 Subject: [PATCH 298/528] adding easyconfigs: Inspector-2022.0.0.eb --- .../i/Inspector/Inspector-2022.0.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb new file mode 100644 index 00000000000..430cc62b2d4 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Inspector' +version = '2022.0.0' + +homepage = 'https://software.intel.com/en-us/inspector' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] +checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 8733a8a3ad56dae9b2c18380229f4fc4a590b48c Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:18:37 +0100 Subject: [PATCH 299/528] adding easyconfigs: Blender-3.0.0-binary.eb --- .../b/Blender/Blender-3.0.0-binary.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb new file mode 100644 index 00000000000..8de30bc9841 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb @@ -0,0 +1,36 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.0.0' +versionsuffix = '-binary' + +homepage = 'https://www.blender.org' +description = """ +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, +modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video +editing and game creation. +""" + +toolchain = SYSTEM + +source_urls = ['http://ftp.nluug.nl/pub/graphics/%(namelower)s/release/%(name)s%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s-linux-x64.tar.xz'] +checksums = ['19b09dfcf5d3f3a068827454f0a704a9aa9c826350f73016121afef5f4d287ce'] + +dependencies = [ + ('CUDA', '11.4.1'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['%(version_major_minor)s'], +} + +modaliases = { + 'blender': 'blender -- --cycles-device CUDA', +} + +moduleclass = 'vis' From 104ae9b2daa603e3cf327de509b3e307bb70d251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:32:15 +0100 Subject: [PATCH 300/528] complete rename of NGS Python bindings to NGS-Python --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- .../NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 487026ab37c..da30bd94a9d 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('pytest', '3.8.2', versionsuffix), - ('NGS', '2.9.3', versionsuffix), # required for srastream + ('NGS-Python', '2.9.3', versionsuffix), # required for srastream ] use_pip = True diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index 410071ff7cb..e8a898cc830 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -12,10 +12,11 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['NGS-%(version)s_fix-python-install-prefix.patch'] +patches = ['NGS-Python-%(version)s_fix-python-install-prefix.patch'] checksums = [ 'd16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d', # 2.9.3.tar.gz - '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', # NGS-2.9.3_fix-python-install-prefix.patch + # NGS-Python-2.9.3_fix-python-install-prefix.patch + '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', ] dependencies = [('Python', '3.6.6')] From 0f9b6995381b2966020093c968b91a65ce40d1c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:39:27 +0100 Subject: [PATCH 301/528] fix name + custom sanity check for NGS-Python 2.9.3 --- .../NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index e8a898cc830..3ef4112bbde 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'NGS' +name = 'NGS-Python' version = '2.9.3' versionsuffix = '-Python-%(pyver)s' @@ -38,4 +38,11 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +sanity_check_paths = { + 'files': [], + 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share/examples'], +} + +sanity_check_commands = ["python -c 'import ngs'"] + moduleclass = 'bio' From 6d275469954f22188052b46531cf3d445d7673b6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:40:04 +0100 Subject: [PATCH 302/528] adding easyconfigs: DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb, DualSPHysics-5.0.175-GCC-11.2.0.eb and patches: DualSPHysics-5.0.175.patch --- ...SPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 65 +++++++++++++++++++ .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 59 +++++++++++++++++ .../d/DualSPHysics/DualSPHysics-5.0.175.patch | 25 +++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..cc55298e964 --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,65 @@ +## +# Authors: Eduardo Miguel Firvida Donestevez +# Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'DualSPHysics' +version = '5.0.175' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://dual.sphysics.org/' + +description = """ +DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + +The code is developed to study free-surface flow phenomena where Eulerian methods +can be difficult to apply, such as waves or impact of dam-breaks on off-shore +structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal +with real-life engineering problems. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s.patch'] +checksums = [ + 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', + '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', +] + +srcdir = 'src/source' + +builddependencies = [ + ('CUDA', '11.4.1', '', True), + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" + +install_cmd = """mkdir -p %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" + + +sanity_check_paths = { + 'files': [ + 'bin/GenCase_linux64', + 'bin/PartVTK_linux64', + 'bin/IsoSurface_linux64', + 'bin/MeasureTool_linux64', + 'bin/GenCase_MkWord_linux64', + 'bin/DualSPHysics4.0_LiquidGas_linux64', + 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', + 'bin/DualSPHysics5.0_linux64', + 'bin/DualSPHysics5.0CPU_linux64', + 'bin/DualSPHysics5.0_NNewtonian_linux64', + 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', + ], + 'dirs': ["lib", "bin"], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb new file mode 100644 index 00000000000..ca2d9e47fbd --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -0,0 +1,59 @@ +## +# Authors: Eduardo Miguel Firvida Donestevez +# Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'DualSPHysics' +version = '5.0.175' + +homepage = 'https://dual.sphysics.org/' + +description = """ +DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + +The code is developed to study free-surface flow phenomena where Eulerian methods +can be difficult to apply, such as waves or impact of dam-breaks on off-shore +structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal +with real-life engineering problems. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575'] + +srcdir = 'src/source' + +builddependencies = [ + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" + +install_cmd = """mkdir -p %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" + + +sanity_check_paths = { + 'files': [ + 'bin/GenCase_linux64', + 'bin/PartVTK_linux64', + 'bin/IsoSurface_linux64', + 'bin/MeasureTool_linux64', + 'bin/GenCase_MkWord_linux64', + 'bin/DualSPHysics4.0_LiquidGas_linux64', + 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', + 'bin/DualSPHysics5.0_linux64', + 'bin/DualSPHysics5.0CPU_linux64', + 'bin/DualSPHysics5.0_NNewtonian_linux64', + 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', + ], + 'dirs': ["lib", "bin"], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch new file mode 100644 index 00000000000..556373c9719 --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch @@ -0,0 +1,25 @@ +diff -Naur DualSPHysics-5.0.175/src/source/CMakeLists.txt DualSPHysics-5.0.175/src/source/CMakeLists.txt +--- DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-02-25 18:46:13.000000000 +0100 ++++ DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-10-13 18:46:17.000000000 +0200 +@@ -52,9 +52,12 @@ + elseif(CUDA_VERSION VERSION_GREATER "7.4" AND CUDA_VERSION VERSION_LESS "9.1") + message("Using cuda version >=7.5 and <9.1") + list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_20,code=\"sm_20,compute_20\" -gencode=arch=compute_30,code=\"sm_30,compute_30\" -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\"") +- else() +- message("Using cuda version >=9.1") ++ elseif(CUDA_VERSION VERSION_GREATER "9.1" AND CUDA_VERSION VERSION_LESS "11.1") ++ message("Using cuda version >=9.1 and <11.1") + list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_30,code=\"sm_30,compute_30\" -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\" -gencode=arch=compute_61,code=\"sm_61,compute_61\" -gencode=arch=compute_70,code=\"sm_70,compute_70\"") ++ else() ++ message("Using cuda version >=11.1") ++ list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\" -gencode=arch=compute_61,code=\"sm_61,compute_61\" -gencode=arch=compute_70,code=\"sm_70,compute_70\" -gencode=arch=compute_80,code=\"sm_80,compute_80\"") + endif() + else() + message("CUDA Libraries were not found.") +@@ -201,4 +204,4 @@ + string(REGEX REPLACE "/MD" "/MT" ${CPP_FLAGS} "${${CPP_FLAGS}}") + endif(${CPP_FLAGS} MATCHES "/MD") + endforeach(CPP_FLAGS) +-endif() +\ No newline at end of file ++endif() From 4c8bf75fede73971f9859ac69b0ef4e8568cb425 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:41:11 +0100 Subject: [PATCH 303/528] enable sanity_pip_check + add custom sanity check command for atropos + strip out standard PyPI source URLs --- .../atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index da30bd94a9d..63b3eb72f6e 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -20,52 +20,40 @@ use_pip = True exts_list = [ ('python-utils', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-utils/'], 'checksums': ['34aaf26b39b0b86628008f2ae0ac001b30e7986a8d303b61e1357dfcdad4f6d3'], }), ('progressbar2', '3.39.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar2/'], 'checksums': ['6eb5135b987caca4212d2c7abc2923d4ad5ba18bb34ccbe7044b3628f52efc2c'], 'modulename': 'progressbar', }), ('tqdm', '4.31.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], }), ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file/'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('screed', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/screed/'], 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], }), ('khmer', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/khmer/'], 'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('pokrok', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pokrok'], 'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'], }), ('xphyle', '4.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xphyle/'], 'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'], }), ('srastream', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/srastream/'], 'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/atropos/'], 'checksums': ['8178af467734b299960edae15d8835a2228ba0cc1b718af436c7d86041fbd4ec'], }), ] @@ -75,4 +63,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["atropos --help"] + +sanity_pip_check = True + moduleclass = 'bio' From 407b034464f16c26f4da12ea111f2916c7c8c38d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:54:12 +0100 Subject: [PATCH 304/528] AMD-uProf: fixes indent problem --- easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb index 37ec97a3ea8..e39f360a639 100644 --- a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -26,7 +26,7 @@ sanity_check_paths = { sanity_check_commands = ['AMDuProfCLI info --system'] modextrapaths = { - 'LD_LIBRARY_PATH': 'bin' + 'LD_LIBRARY_PATH': 'bin' } moduleclass = 'perf' From c1f2aa125ee6fa8c53268a5dbc1827a5de196901 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 17:38:12 +0100 Subject: [PATCH 305/528] fix duplicate sanity_check_paths in NGS-Python easyconfig --- .../NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index 3ef4112bbde..59aa5296d86 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -33,16 +33,11 @@ parallel = 1 sanity_check_paths = { 'files': ['lib64/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-adapt-c++.a', 'lib64/libngs-c++.a'], - 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': [], 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share/examples'], } sanity_check_commands = ["python -c 'import ngs'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'bio' From b84eef788364c13c5dab3293871a15b6712e1b42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 20:50:11 +0100 Subject: [PATCH 306/528] fix sanity check command for atropos --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 63b3eb72f6e..3cb07d04e5e 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -63,7 +63,7 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["atropos --help"] +sanity_check_commands = ["atropos detect --help"] sanity_pip_check = True From 2be5e2e0aa31f853baa82df8f45ab861181e7c13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 21:20:21 +0100 Subject: [PATCH 307/528] enable sanity_pip_check in easyconfig for CVXOPT 1.2.3 --- .../c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb index f3d00fec42d..2b5c5824d8c 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'CVXOPT' version = '1.2.3' @@ -13,7 +13,6 @@ description = """CVXOPT is a free software package for convex optimization based toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'pic': True} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] checksums = [ @@ -37,9 +36,6 @@ installopts = ' --no-binary cvxopt' postinstallcmds = ['nosetests'] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_pip_check = True moduleclass = 'math' From 84b9fb7278af0295f23a4a43deda48d97eaeb10e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 09:23:45 +0100 Subject: [PATCH 308/528] Fix description (which was referring to AMD-RNG) --- easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb index e39f360a639..f725f56d505 100644 --- a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -7,7 +7,9 @@ name = 'AMD-uProf' version = '3.4.502' homepage = 'https://developer.amd.com/amd-uprof/' -description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" +description = """AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD + operating systems. It allows developers to better understand the runtime performance of their application and + to identify ways to improve its performance.""" toolchain = SYSTEM From 4515a1cb24892dd589ccb9ac1c85647336707aba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 10:51:38 +0100 Subject: [PATCH 309/528] add simple sanity check command --- easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb index 75cf15432a6..05722624103 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['muscle -version'] + moduleclass = 'bio' From de826311b825fe20a1747e2d2ccb68235158e336 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 11:07:42 +0100 Subject: [PATCH 310/528] run nosetests as sanity check command in CVXOPT 1.2.3 easyconfig --- .../c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb index 2b5c5824d8c..60b0fae0eda 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -34,8 +34,8 @@ preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_ installopts = ' --no-binary cvxopt' -postinstallcmds = ['nosetests'] - sanity_pip_check = True +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] + moduleclass = 'math' From e6951e3bebe70726b5d3f228c35f371b9dec7cda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 11:09:44 +0100 Subject: [PATCH 311/528] use toolchain's default muscle version --- easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index a0c8a90bc51..db39bb21b3b 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('GlimmerHMM', '3.0.4c'), ('HMMER2', '2.3.2'), ('HMMER', '3.3.2'), - ('MUSCLE', '3.8.1551'), + ('MUSCLE', '3.8.31'), ('BLAST+', '2.11.0'), ('prodigal', '2.6.3'), ('Biopython', '1.78'), From 8168d875a1e2737524f5febbeecc089788819e85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 11:18:51 +0100 Subject: [PATCH 312/528] remove unused MUSCLE easyconfig --- .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb deleted file mode 100644 index 05722624103..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = "3.8.1551" - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCC', 'version': '10.2.0'} - -source_urls = ['https://www.drive5.com/muscle/'] -sources = ['%(namelower)s_src_%(version)s.tar.gz'] -checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] - -# use correct compiler flags + -# don't use -static when linking, since that implies requiring glibc-static to be installed -buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' - -files_to_copy = [(["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/%(namelower)s"], - 'dirs': [], -} - -sanity_check_commands = ['muscle -version'] - -moduleclass = 'bio' From bca2df9228a35ea346b7e08e3e0f897254298ee1 Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Fri, 24 Dec 2021 11:21:43 +0100 Subject: [PATCH 313/528] Update Julia v1.7.1 --- .../j/Julia/Julia-1.7.1-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb new file mode 100644 index 00000000000..79469033db5 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.7.1' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From d119f7934a3ef20616f820f87b8560cda8795f35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 17:09:34 +0100 Subject: [PATCH 314/528] revert changes to archived GLIMMER easyconfigs --- .../__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 5 ++--- .../__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index da9c09fd6d5..9224bccf7f9 100644 --- a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -11,15 +11,14 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' +homepage = 'http://www.cbcb.umd.edu/software/glimmer/' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] +source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index 49bd7675820..90a24de0cf2 100644 --- a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -11,15 +11,14 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' +homepage = 'http://www.cbcb.umd.edu/software/glimmer/' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] +source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' From e0ed983df9ccfd2ba92454a84e6088f6d938a133 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 17:22:45 +0100 Subject: [PATCH 315/528] add SHA256 checksum for both original and current source tarballs of GLIMMER 3.02b + add sanity check command --- .../easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 8 ++++++-- .../easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 8 ++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 59dcbaec249..56c96e97fcf 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -19,15 +19,19 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] +# original source tarball did not have a README file, but no other changes in source files +checksums = [('a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3', + 'ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6')] buildopts = '-C ./src' files_to_copy = ['bin', 'docs', 'glim302notes.pdf', 'lib', 'LICENSE', 'sample-run', 'scripts'] sanity_check_paths = { - 'files': ['bin/%(namelower)s3', 'glim302notes.pdf', 'LICENSE'], + 'files': ['bin/glimmer3', 'glim302notes.pdf', 'LICENSE'], 'dirs': ['docs', 'lib', 'sample-run', 'scripts'], } +sanity_check_commands = ["glimmer3 --help 2>&1 | grep 'USAGE:[ ]*glimmer3'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index 1c389bd393d..34ccceea479 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -20,15 +20,19 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] +# original source tarball did not have a README file, but no other changes in source files +checksums = [('a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3', + 'ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6')] buildopts = "-C ./src" files_to_copy = ['bin', 'docs', 'glim302notes.pdf', 'lib', 'LICENSE', 'sample-run', 'scripts'] sanity_check_paths = { - 'files': ['bin/%(namelower)s3', 'glim302notes.pdf', 'LICENSE'], + 'files': ['bin/glimmer3', 'glim302notes.pdf', 'LICENSE'], 'dirs': ['docs', 'lib', 'sample-run', 'scripts'], } +sanity_check_commands = ["glimmer3 --help 2>&1 | grep 'USAGE:[ ]*glimmer3'"] + moduleclass = 'bio' From c758811238ea8dfcfd2b08f60be7bc2981983faf Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:41:47 +0100 Subject: [PATCH 316/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index cc55298e964..f69e5fa9796 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -10,14 +10,12 @@ versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://dual.sphysics.org/' -description = """ -DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. +description = """DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. -The code is developed to study free-surface flow phenomena where Eulerian methods -can be difficult to apply, such as waves or impact of dam-breaks on off-shore -structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal -with real-life engineering problems. -""" + The code is developed to study free-surface flow phenomena where Eulerian methods + can be difficult to apply, such as waves or impact of dam-breaks on off-shore + structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal + with real-life engineering problems.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From 1993270ed6a3884b04ae0c9d484790482a44773d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:41:58 +0100 Subject: [PATCH 317/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index f69e5fa9796..20cd2d89b41 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -38,9 +38,9 @@ separate_build_dir = True buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" -install_cmd = """mkdir -p %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" +install_cmd = "mkdir -p %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" sanity_check_paths = { From 2893bdc8e5fce83db4b50d28d6948d7505b019a6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:17 +0100 Subject: [PATCH 318/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 20cd2d89b41..64826f054a5 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -57,7 +57,7 @@ sanity_check_paths = { 'bin/DualSPHysics5.0_NNewtonian_linux64', 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', ], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } moduleclass = 'cae' From 0860e551f5ded6c54060300c772b8c3f2c96fd5e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:26 +0100 Subject: [PATCH 319/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index ca2d9e47fbd..495ea2289e2 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -9,14 +9,12 @@ version = '5.0.175' homepage = 'https://dual.sphysics.org/' -description = """ -DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. - -The code is developed to study free-surface flow phenomena where Eulerian methods -can be difficult to apply, such as waves or impact of dam-breaks on off-shore -structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal -with real-life engineering problems. -""" +description = """DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + + The code is developed to study free-surface flow phenomena where Eulerian methods + can be difficult to apply, such as waves or impact of dam-breaks on off-shore + structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal + with real-life engineering problems.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From eccbbc81cfdeb905513892015ce4eb0e8ccc58c3 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:51 +0100 Subject: [PATCH 320/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 64826f054a5..33a9ac4cc9f 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -23,8 +23,8 @@ source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/' sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s.patch'] checksums = [ - 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', - '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', + 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', # v5.0.175.tar.gz + '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', # DualSPHysics-5.0.175.patch ] srcdir = 'src/source' From 69ab4b22f889a6556b9dc14188a84e8e5c810c0b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:44:06 +0100 Subject: [PATCH 321/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index 495ea2289e2..f2c7ad44957 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -51,7 +51,7 @@ sanity_check_paths = { 'bin/DualSPHysics5.0_NNewtonian_linux64', 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', ], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } moduleclass = 'cae' From 2caa2d7adf918471ca1df0cd070bbcaf67007442 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:04:46 +0100 Subject: [PATCH 322/528] add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 2f1d783930e..311a8b3d71c 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3178,6 +3178,24 @@ exts_list = [ ('covsim', '0.2.1', { 'checksums': ['57ca810c6950ab295078b745eb87fdd7f195e15082777eed9f1059b6302f13bf'], }), + ('semTools', '0.5-5', { + 'checksums': ['ddf883753c5964eae8313d7e8a4703be52e649f10d3bc1d12ede6d1707b1fab6'], + }), + ('GPArotation', '2014.11-1', { + 'checksums': ['351bc15fc8dc6c8ea5045fbba22180d1e68314fc34d267545687748e312e5096'], + }), + ('dcurver', '0.9.2', { + 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], + }), + ('mirt', '1.35.1', { + 'checksums': ['788b7e499b7d48f5f590eb5cfdac260c4e993b94a3956d30bc2d8bce8cd2ba3e'], + }), + ('rpf', '1.0.11', { + 'checksums': ['e1fd670ae7c3e947db08ce50d6b16ce1b3b8f63a9016b03baba760aee78921fb'], + }), + ('OpenMx', '2.19.8', { + 'checksums': ['cb4be9850f61d320dcd47ef0ad7b20e5baafde558ebbc67301b13d883baf6760'], + }), ] moduleclass = 'lang' From fda6b0611b83b9ea3786c162e1ca92762df75138 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:08:23 +0100 Subject: [PATCH 323/528] remove whitespace from empty line --- .../dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb index 20136cc0efc..3316dc777fe 100644 --- a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ description = """.NET is a free, cross-platform, open source developer platform of applications.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - + source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + 'be8a513c-f3bb-4fbd-b382-6596cf0d67b5/968e205c44eabd205b8ea98be250b880'] sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] From c53f936f88a744ed557d065026eb645d23d8cf43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:13:09 +0100 Subject: [PATCH 324/528] add back notes to header of dotNET-SDK easyconfig --- .../easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb index 7e1702a66c2..c98b7621f4e 100644 --- a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -1,6 +1,9 @@ ## # Authors:: Robert Qiao # Robert Mijakovic +# +# License:: MIT +# Notes:: requires glibc v2.14 or higher ## easyblock = 'Tarball' From 345afb717cedff80ed650c02a6b9ef6197f923d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:13:59 +0100 Subject: [PATCH 325/528] add sanity check command for dotNET-Core-Runtime --- .../dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb index 3316dc777fe..2959307e390 100644 --- a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -25,6 +25,8 @@ sanity_check_paths = { 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], } +sanity_check_commands = ["dotnet --info"] + modextrapaths = {'PATH': ['']} moduleclass = 'lang' From e8f48252d587bdf4dae5fcbea4b4db84ca76631d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:17:13 +0100 Subject: [PATCH 326/528] add sanity check command for dotNET-SDK --- .../easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb index c98b7621f4e..26301f192c6 100644 --- a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -26,6 +26,8 @@ sanity_check_paths = { 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], } +sanity_check_commands = ["dotnet --help"] + modextrapaths = { 'PATH': [''], 'DOTNET_ROOT': [''], From bce4df2af9fae86a2b19a496f021c1917881326b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Dec 2021 11:33:06 +0100 Subject: [PATCH 327/528] adding easyconfigs: ParaView-5.9.1-foss-2021b-mpi.eb and patches: ParaView-5.9.1_fix-GCC-11.patch --- .../ParaView/ParaView-5.9.1-foss-2021b-mpi.eb | 62 +++++++++++++++++++ .../ParaView/ParaView-5.9.1_fix-GCC-11.patch | 47 ++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb new file mode 100644 index 00000000000..c131ad80db0 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb @@ -0,0 +1,62 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.9.1' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.9.1_fix-GCC-11.patch'] +checksums = [ + 'efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f', # ParaView-v5.9.1.tar.gz + '771cf0974333833bbed2bbb573a5782725ae8564d85901e68e6a826972512104', # ParaView-5.9.1_fix-GCC-11.patch +] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('XZ', '5.2.5'), + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('libGLU', '9.0.2'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch new file mode 100644 index 00000000000..0663afb6edc --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch @@ -0,0 +1,47 @@ +fix compilation with GCC 11, fixes compilation errors like: + error: numeric_limits is not a member of std +author: Kenneth Hoste (HPC-UGent) +diff -ru ParaView-v5.9.1.orig/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h ParaView-v5.9.1/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h +--- ParaView-v5.9.1.orig/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h 2021-12-23 11:07:09.825480119 +0100 +@@ -25,6 +25,7 @@ + #include "vtkIdList.h" + #include + #include ++#include + #include + #include + +diff -ru ParaView-v5.9.1.orig/VTK/Common/DataModel/vtkPiecewiseFunction.cxx ParaView-v5.9.1/VTK/Common/DataModel/vtkPiecewiseFunction.cxx +--- ParaView-v5.9.1.orig/VTK/Common/DataModel/vtkPiecewiseFunction.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Common/DataModel/vtkPiecewiseFunction.cxx 2021-12-23 11:07:41.295765924 +0100 +@@ -22,6 +22,7 @@ + #include + #include + #include ++#include + #include + #include + +diff -ru ParaView-v5.9.1.orig/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx ParaView-v5.9.1/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx +--- ParaView-v5.9.1.orig/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx 2021-12-23 11:07:51.895861970 +0100 +@@ -27,6 +27,7 @@ + #include "vtkHyperTreeGridNonOrientedCursor.h" + + #include ++#include + + vtkStandardNewMacro(vtkHyperTreeGridThreshold); + +diff -ru ParaView-v5.9.1.orig/VTK/Rendering/Core/vtkColorTransferFunction.cxx ParaView-v5.9.1/VTK/Rendering/Core/vtkColorTransferFunction.cxx +--- ParaView-v5.9.1.orig/VTK/Rendering/Core/vtkColorTransferFunction.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Rendering/Core/vtkColorTransferFunction.cxx 2021-12-23 11:07:25.985627071 +0100 +@@ -21,6 +21,7 @@ + #include + #include + #include ++#include + #include + #include + From 63956ba9f05d56f030129532c4ad694e38bc9be3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Dec 2021 11:39:09 +0100 Subject: [PATCH 328/528] adding easyconfigs: OpenFOAM-v2112-foss-2021b.eb, CGAL-4.14.3-gompi-2021b.eb, SCOTCH-6.1.2-gompi-2021b.eb --- .../c/CGAL/CGAL-4.14.3-gompi-2021b.eb | 37 ++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb | 42 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb | 22 ++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb new file mode 100644 index 00000000000..b41d2e7d755 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.14.3' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.6'), + ('Boost', '1.77.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.2'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb new file mode 100644 index 00000000000..324e545e4b5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb @@ -0,0 +1,42 @@ +name = 'OpenFOAM' +version = 'v2112' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.21.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('CGAL', '4.14.3'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb new file mode 100644 index 00000000000..88bf9265ec8 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'SCOTCH' +version = '6.1.2' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 91384df6b9b1131e864789757aa6d964be173483 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Dec 2021 13:33:05 +0100 Subject: [PATCH 329/528] adding easyconfigs: SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb --- ...10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..3b0648e9b1f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +local_cuda_ver = '11.3.1' +versionsuffix = '-METIS-%s-CUDA-%s' % (local_metis_ver, local_cuda_ver) + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), + ('CUDA', local_cuda_ver, '', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 69d4881866ae6f48e516109d190511feb4da8095 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Dec 2021 13:39:13 +0100 Subject: [PATCH 330/528] use cudaver --- .../SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb index 3b0648e9b1f..2ef23ba8a82 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -1,8 +1,7 @@ name = 'SuiteSparse' version = '5.10.1' local_metis_ver = '5.1.0' -local_cuda_ver = '11.3.1' -versionsuffix = '-METIS-%s-CUDA-%s' % (local_metis_ver, local_cuda_ver) +versionsuffix = '-METIS-%s-CUDA-%%(cudaver)s' % local_metis_ver homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -22,7 +21,7 @@ builddependencies = [ dependencies = [ ('METIS', local_metis_ver), ('MPFR', '4.1.0'), - ('CUDA', local_cuda_ver, '', True), + ('CUDA', '11.3.1', '', True), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From 98d789bf3f1fa8dd8cc9681db841b5db585e0bb0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 29 Dec 2021 09:12:02 +0100 Subject: [PATCH 331/528] adding easyconfigs: OBITools-1.2.13-foss-2019a-Python-2.7.15.eb --- ...BITools-1.2.13-foss-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..97e6acc1884 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'OBITools' +version = '1.2.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://git.metabarcoding.org/obitools/obitools/wikis/home' +description = """OBITools is a set of python programs developed to +simplify the manipulation of sequence files. They were mainly designed +to for analyzing Next Generation Sequencer outputs (454 or Illumina) in +the context of DNA Metabarcoding.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['efc7b583a44f435f0663f9d67759a0e3d415ba1896e6132198cb135e35c34873'] + +dependencies = [ + ('Python', '2.7.15'), + ('IPython', '5.8.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'obitools'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ali2consensus', 'ecotag', 'obiaddtaxids', 'obicount', 'obistat']], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/obitools'], +} + +moduleclass = 'bio' From 62ddcb8a58476b6ec29c9e97a0c23b2cb5318c65 Mon Sep 17 00:00:00 2001 From: kErica Date: Wed, 29 Dec 2021 14:47:05 +0000 Subject: [PATCH 332/528] fix according to lexming review --- .../c/Carma/Carma-2.01-foss-2019b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb new file mode 100644 index 00000000000..20eedb9845c --- /dev/null +++ b/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb @@ -0,0 +1,33 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco +# License:: GPL-v3.0 +# # + +easyblock = 'CmdCp' + +name = 'Carma' +version = '2.01' + +homepage = 'http://utopia.duth.gr/~glykos/Carma.html' +description = """Carma - A molecular dynamics analysis program""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['http://utopia.duth.gr/~glykos/progs/'] +sources = ['%(namelower)s.tar.gz'] +checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] + +start_dir = 'src' +cmds_map = [('.*', "$CC $CFLAGS -O -c Color_carma.c && $FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma")] +files_to_copy = [(['carma'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/carma'], + 'dirs': [''], +} + +sanity_check_commands = ['carma'] + +moduleclass = 'chem' From a0738f3904dd2013efd07936fe9d56d67a2dd980 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Wed, 29 Dec 2021 15:47:38 +0100 Subject: [PATCH 333/528] drop lowercase version --- .../c/carma/carma-2.01-foss-2019b.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb deleted file mode 100644 index 40bf7dc47da..00000000000 --- a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb +++ /dev/null @@ -1,34 +0,0 @@ -# # -# This is a contribution from HPCNow! (http://hpcnow.com) -# Copyright:: HPCNow! -# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco -# License:: GPL-v3.0 -# # - -easyblock = 'Tarball' - -name = 'carma' -version = '2.01' - -homepage = 'http://utopia.duth.gr/~glykos/Carma.html' -description = """carma - A molecular dynamics analysis program""" - -toolchain = {'name': 'foss', 'version': '2019b'} - -source_urls = ['http://utopia.duth.gr/~glykos/progs/'] -sources = ['%(name)s.tar.gz'] -checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] - -preinstall_cmd = 'cd %(builddir)s/%(name)s-%(version)s/src && ' -preinstall_cmd += '$CC $CFLAGS -O -c Color_carma.c && ' -preinstall_cmd += '$FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma &&' -preinstall_cmd += 'cp -p carma ../bin/' - -sanity_check_paths = { - 'files': ['bin/carma'], - 'dirs': [''], -} - -tests = ['%(installdir)s/bin/carma'] - -moduleclass = 'lib' From d20d95736e217a87c67a64cd3aa015c8d488c833 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 29 Dec 2021 19:57:00 +0200 Subject: [PATCH 334/528] adding easyconfigs: FTGL-2.1.3-rc5-GCCcore-10.2.0.eb --- .../f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6f17150fb6c --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('freetype', '2.10.3'), + ('libGLU', '9.0.1'), + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL', 'share'] +} + +moduleclass = 'lib' From a8d0c2daa43d111e06a2319b849d6887cced8f88 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 31 Dec 2021 10:02:47 +0100 Subject: [PATCH 335/528] update checksum for Siesta-4.1-MaX-1.0 --- .../s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb | 3 ++- .../easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb index c7bf7ebe69c..d72b952fc2a 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb @@ -12,7 +12,8 @@ toolchainopts = {'usempi': True, 'precise': True} source_urls = ['https://gitlab.com/siesta-project/siesta/-/archive/%s' % _release] sources = ['%%(namelower)s-%s.tar.gz' % _release] -checksums = ['c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881'] +checksums = [('c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881', + '02a00e087fcd24b839bde0060cc1af4b116efa3e52aabe32177dcb6dc332c69b')] dependencies = [ ('ELSI', '2.5.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb index f4becec3ee4..22e245c782f 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb @@ -11,7 +11,8 @@ toolchainopts = {'usempi': True, 'precise': True} source_urls = ['https://gitlab.com/siesta-project/siesta/-/archive/%s' % _release] sources = ['%%(namelower)s-%s.tar.gz' % _release] -checksums = ['c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881'] +checksums = [('c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881', + '02a00e087fcd24b839bde0060cc1af4b116efa3e52aabe32177dcb6dc332c69b')] dependencies = [ ('ELSI', '2.5.0'), From 564a382209d74dbbf8dcc7bf09beb08d606a3da0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 3 Jan 2022 15:06:15 +0100 Subject: [PATCH 336/528] {lib}[foss/2021b] libxsmm 1.17 PLUMED 2.7.3 --- .../l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb | 27 +++++++++ .../p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 56 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb new file mode 100644 index 00000000000..d459d902f56 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb new file mode 100644 index 00000000000..5e10ec4a8f3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.3' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['2895515f31aae42002a539222f5b8558037496548a061b5d0db136d3a46f618b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 8f4396c9d6d6d69d07eba565a706d6d513a7bc7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jan 2022 12:15:38 +0100 Subject: [PATCH 337/528] update Java 1.8 wrapper to 1.8.0_311 for x86_64 --- easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb | 17 +++++++++++++++++ easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb new file mode 100644 index 00000000000..47bc761cc52 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb @@ -0,0 +1,17 @@ +name = 'Java' +version = '1.8.0_311' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(local_vp, local_vs) = version.split('_') +local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) +sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] +checksums = ['759823389014292e84742a226b0e8fbaa08efa32adc6e6435a690c5576df3bb4'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 63e9532dd32..ed823a63205 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -14,7 +14,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM dependencies = [ - ('Java', {'arch=x86_64': '%(version)s.0_281', + ('Java', {'arch=x86_64': '%(version)s.0_311', 'arch=POWER': '%(version)s_191-b26-OpenJDK', 'arch=AArch64': '%(version)s_265-b01-OpenJDK-aarch64'}), ] From 6d4fec9222bdb5779bbcd08c7faafbea6b80eb29 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 3 Jan 2022 17:54:52 +0100 Subject: [PATCH 338/528] Update STRUMPACK-6.1.0-foss-2020b.eb and STRUMPACK-6.1.0-intel-2020b.eb Co-authored-by: Alex Domingo --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 16 +++++----------- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 16 +++++----------- 2 files changed, 10 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index 26e9142f8f1..a47c361c4c5 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_ENABLE_BPACK=OFF ' @@ -42,11 +35,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 4938fb4262b..47b5368522d 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' @@ -43,11 +36,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' From bd3aa473d91199c23bf79e8e00b7e454c8b4a57c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 3 Jan 2022 18:51:09 +0000 Subject: [PATCH 339/528] stick to torchvision 0.8.2 as dependency in 2020b --- ...8.1.eb => PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PyTorch3D/{PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb => PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb} (95%) diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb similarity index 95% rename from easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb rename to easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb index 9be26b1a985..28c09209b9c 100644 --- a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'PyTorch3D' version = '0.4.0' -local_pytorch_version = '1.8.1' +local_pytorch_version = '1.7.1' versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = "https://pytorch3d.org/" @@ -17,7 +17,7 @@ dependencies = [ ('PyTorch', local_pytorch_version), ('imageio', '2.9.0'), ('IPython', '7.18.1'), - ('torchvision', '0.9.1', versionsuffix), + ('torchvision', '0.8.2', versionsuffix), ] sanity_pip_check = True From 9208d46e7e094c0b75054bd1218cc79c1ff93076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 10:17:59 +0100 Subject: [PATCH 340/528] add FactorCopula extension for R v4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 311a8b3d71c..add27951e71 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3196,6 +3196,12 @@ exts_list = [ ('OpenMx', '2.19.8', { 'checksums': ['cb4be9850f61d320dcd47ef0ad7b20e5baafde558ebbc67301b13d883baf6760'], }), + ('matlab', '1.0.2', { + 'checksums': ['a23dec736c51ae1864c1a53caac556a2f98e8020138a3b121badb0f5b7984154'], + }), + ('FactorCopula', '0.8', { + 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], + }), ] moduleclass = 'lang' From aebd17a34291c990f873f40dcbeba5a8e7896edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 10:49:24 +0100 Subject: [PATCH 341/528] remove commented out barrnap dependency in SqueezeMeta easyconfig, need to use vendored patched barrnap --- .../s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index 700c3b31af3..e68964c3d36 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -27,7 +27,6 @@ dependencies = [ ('R', '3.5.1', versionsuffix), ('BLAST+', '2.7.1'), ('BWA', '0.7.17'), - #('barrnap', '0.9'), ('CD-HIT', '4.6.8'), ('CheckM', '1.0.13', versionsuffix), ('DAS_Tool', '1.1.1', '-R-%(rver)s-Python-%(pyver)s'), # depends on prodigal & pullseq From cc7b203b0ffdc648036dd5b236829dc424b03373 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:12:14 +0100 Subject: [PATCH 342/528] update $R_LIBS_SITE rather than $R_LIBS in easyconfig for SqueezeMeta 1.0.0 --- .../s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index e68964c3d36..bc932b4a6c7 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -75,7 +75,7 @@ sanity_check_commands = ["""echo 'library("SQMtools")' | R -q --no-save"""] modextrapaths = { 'PATH': 'scripts', - 'R_LIBS': 'R', + 'R_LIBS_SITE': 'R', } moduleclass = 'bio' From 572c0d455142eb5b1cc899a533a9cb0056f65fe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:30:02 +0100 Subject: [PATCH 343/528] adding easyconfigs: XML-LibXML-2.0207-GCCcore-11.2.0.eb --- .../XML-LibXML-2.0207-GCCcore-11.2.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c92e343a475 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0207' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('libxml2', '2.9.10'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1010', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], + }), + ('Alien::Base', '2.46', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4bb301fa2b6296a9d8e285000932ea3340832a3a70bdb9c5e1a63c6fd1cf4a67'], + }), + ('Alien::Libxml2', '0.17', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['73b45244f0b5c36e5332c33569b82a1ab2c33e263f1d00785d2003bcaec68db3'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['903436c9859875bef5593243aae85ced329ad0fb4b57bbf45975e32547c50c15'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From fc7cdb69584b0a371e8ca375655107ad9f912c16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:51:35 +0100 Subject: [PATCH 344/528] add missing PCRE dependency for pullseq + add sanity check commands --- .../easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb index bc6e3f50681..513b5e5c745 100644 --- a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb @@ -16,6 +16,9 @@ builddependencies = [ ('binutils', '2.30'), ('Autotools', '20180311'), ] +dependencies = [ + ('PCRE', '8.41'), +] preconfigopts = "./bootstrap && " @@ -24,4 +27,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + moduleclass = 'bio' From 02232f6529a806275e64f15b0b6428005ce6f4d8 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Jan 2022 13:25:04 +0100 Subject: [PATCH 345/528] adding easyconfigs: CMake-3.22.1-GCCcore-11.2.0.eb --- .../c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7d88407d378 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.22.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0e998229549d7b3f368703d20e248e7ee1f853910d42704aa87918c213ea82c0'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.78.0'), + ('libarchive', '3.5.1'), + ('OpenSSL', '1.1', '', True), +] + +moduleclass = 'devel' From ecc1c7769517e0aa883afba1a58746de9f2dd2fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 4 Jan 2022 13:45:59 +0100 Subject: [PATCH 346/528] adding easyconfigs: AdapterRemoval-2.3.2-GCC-11.2.0.eb --- .../AdapterRemoval-2.3.2-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..4ba0d0fbca4 --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From f8206a625b357eba04ab27e5c351fa7a8886cd38 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 4 Jan 2022 15:15:03 +0100 Subject: [PATCH 347/528] Patch CHERAB/1.3.0 for intel/2020b and foss/2020b --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 31 +++++++++++++++++++ .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 13 ++++---- 2 files changed, 37 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb new file mode 100644 index 00000000000..bb77bca7706 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index 7d3d731a92e..c0847561d7d 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,7 +11,11 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] dependencies = [ ('Python', '3.8.6'), @@ -22,11 +26,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = False - -sanity_check_commands = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' - 'python -c "import cherab"' -] +sanity_pip_check = True moduleclass = 'phys' From 483d8e6d10ff9163cea988643e5fde45323da8d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 17:31:54 +0100 Subject: [PATCH 348/528] use %(arch)s template to avoid hardcoding x86_64 in XML-LibXML easyconfig --- .../x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb index c92e343a475..cf5ef24b6c7 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From e65c68ba8e83f051746908615edade30b68965b6 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 4 Jan 2022 16:39:09 +0000 Subject: [PATCH 349/528] Bazel for GCCcore11 --- .../b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../b/Bazel/gcc11-2-bazel-3.7.2.patch | 10 +++++ .../b/Bazel/gcc11-bazel-3.7.2.patch | 10 +++++ easybuild/easyconfigs/b/Bazel/java15.patch | 29 ++++++++++++ 4 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch create mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch create mode 100644 easybuild/easyconfigs/b/Bazel/java15.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..92bf8614231 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +name = 'Bazel' +version = '3.7.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + '%(name)s-3.4.1-fix-grpc-protoc.patch', + 'java15.patch', + '%(name)s-3.7.1_fix-protobuf-env.patch', + 'gcc11-bazel-3.7.2.patch', + 'gcc11-2-bazel-3.7.2.patch', + +] +checksums = [ + # bazel-3.7.2-dist.zip + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', + # Bazel-3.4.1-fix-grpc-protoc.patch + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', + '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # java15.patch + # Bazel-3.7.1_fix-protobuf-env.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', + # gcc11-bazel-3.7.2.patch + '32dc4abdc45bfcf70e9d93a66150b89646c801f8704930f0b713038366e40d40', + # gcc11-2-bazel-3.7.2.patch + '3160caff050330e33df1f7afb649e8303bf4af969ef7722639bd0f3c3ae036b4', +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('Zip', '3.0'), +] + +prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " +configopts = "--host_jvm_args=--illegal-access=debug" +dependencies = [('Java', '13', '', True)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch new file mode 100644 index 00000000000..c7ceaa84318 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch @@ -0,0 +1,10 @@ +--- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 ++++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 +@@ -16,6 +16,7 @@ + #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H + + #include "third_party/ijar/common.h" ++#include + + namespace devtools_ijar { + diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch new file mode 100644 index 00000000000..b46eda73836 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch @@ -0,0 +1,10 @@ +--- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 ++++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 +@@ -16,6 +16,7 @@ + #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ + + #include ++#include + + #include "third_party/ijar/common.h" + diff --git a/easybuild/easyconfigs/b/Bazel/java15.patch b/easybuild/easyconfigs/b/Bazel/java15.patch new file mode 100644 index 00000000000..6fc6a95634e --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/java15.patch @@ -0,0 +1,29 @@ +From 0216ee54417fa1f2fef14f6eb14cbc1e8f595821 Mon Sep 17 00:00:00 2001 +From: philwo +Date: Mon, 8 Feb 2021 10:45:50 -0800 +Subject: [PATCH] Fix Bazel #10214: JDK 13 introduced a source compatibility + issue. + +Quote from the Java release notes: + +The addition of newFileSystem(Path, Map) creates a source (but not binary) compatibility issue for code that has been using the existing 2-arg newFileSystem(Path, ClassLoader) and specifying the class loader as null. [...] To avoid the ambiguous reference, this code needs to be modified to cast the second parameter to java.lang.ClassLoader. + +RELNOTES: +PiperOrigin-RevId: 356301318 +--- + .../com/google/devtools/build/buildjar/VanillaJavaBuilder.java | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java +index 327017362626..5edf9ba0cf23 100644 +--- a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java ++++ b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java +@@ -77,7 +77,7 @@ + private FileSystem getJarFileSystem(Path sourceJar) throws IOException { + FileSystem fs = filesystems.get(sourceJar); + if (fs == null) { +- filesystems.put(sourceJar, fs = FileSystems.newFileSystem(sourceJar, null)); ++ filesystems.put(sourceJar, fs = FileSystems.newFileSystem(sourceJar, (ClassLoader) null)); + } + return fs; + } \ No newline at end of file From ff63411c0f025ec053a3be6f6e6c6b826befdd65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 19:56:53 +0100 Subject: [PATCH 350/528] use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs --- .../easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb | 2 +- .../x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb | 2 +- .../x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb index 4676ae13f4b..78769aba0ee 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb @@ -46,7 +46,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index ee314c18f7d..62cc7c77d12 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb index 1ce2f4c107a..8cf20d98f03 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From 5dc9ea211ad9f6a2a471c343948d2e49f61ac5cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 07:24:41 +0100 Subject: [PATCH 351/528] adding easyconfigs: PEAR-0.9.11-GCC-11.2.0.eb --- .../p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb new file mode 100644 index 00000000000..4dadb6ab88e --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.11' + +homepage = 'https://cme.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# Needs manual download via web-form, +# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +sources = ['%(namelower)s-src-%(version)s.tar.gz'] +checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = 'aclocal && autoconf && automake --add-missing && ' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 525f695147d5c018eacad159fadec63a570f3a46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:13:12 +0100 Subject: [PATCH 352/528] adding easyconfigs: GffCompare-0.12.6-GCC-11.2.0.eb --- .../GffCompare-0.12.6-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..7146893a15f --- /dev/null +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GffCompare' +version = '0.12.6' + +# Some docs also at GitHub site - this is referred to as canonical +homepage = 'https://ccb.jhu.edu/software/stringtie/gffcompare.shtml' +description = """GffCompare provides classification and reference annotation mapping and + matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +# Switched to GitHub sources owing to SSL error at original download site +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0e713bc9177d874c935802d11669776da5e9377a8c4d031153b48a783d3391d0'] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From 377a0d5ebf85faa39e6a1c7b1e24a763f269e3ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:18:46 +0100 Subject: [PATCH 353/528] adding easyconfigs: gffread-0.12.7-GCC-11.2.0.eb --- .../g/gffread/gffread-0.12.7-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..5a9362d9dee --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' From 4da8e3c4b7bcdf1f6f08ccf0bfff686afcfbc4e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:28:04 +0100 Subject: [PATCH 354/528] adding easyconfigs: KronaTools-2.8.1-GCC-11.2.0.eb --- .../KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3a0d49adac1 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8.1' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.34.0')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From 7e3b37f5afb599e21b9bbf87cf60dcc78b349942 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 09:07:31 +0100 Subject: [PATCH 355/528] change toolchain to GCCcore because there are only scripts and nothing to compile --- ...s-2.8.1-GCC-11.2.0.eb => KronaTools-2.8.1-GCCcore-11.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/k/KronaTools/{KronaTools-2.8.1-GCC-11.2.0.eb => KronaTools-2.8.1-GCCcore-11.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb index 3a0d49adac1..25657b328af 100644 --- a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' description = """Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s.tar'] From e7052b79ca706a32ef12d6973ad376c9b91fde3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 09:13:45 +0100 Subject: [PATCH 356/528] change toolchain to GCCcore --- ...-0.12.7-GCC-11.2.0.eb => gffread-0.12.7-GCCcore-11.2.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/gffread/{gffread-0.12.7-GCC-11.2.0.eb => gffread-0.12.7-GCCcore-11.2.0.eb} (89%) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb similarity index 89% rename from easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb rename to easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb index 5a9362d9dee..0123e140499 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb @@ -8,13 +8,15 @@ homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] +builddependencies = [('binutils', '2.37')] + buildopts = " release" files_to_copy = [ From 4005cafde9ecbbe2380d903a646769bb64f1ef5a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 5 Jan 2022 16:48:53 +0800 Subject: [PATCH 357/528] bring gffread back down to GCCcore level for toolchain version 10.3.0 --- ...-0.12.7-GCC-10.3.0.eb => gffread-0.12.7-GCCcore-10.3.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/gffread/{gffread-0.12.7-GCC-10.3.0.eb => gffread-0.12.7-GCCcore-10.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb similarity index 88% rename from easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb rename to easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb index 0b1607a0ada..2de4e4299bb 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb @@ -8,13 +8,15 @@ homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] +builddependencies = [('binutils', '2.36.1')] + buildopts = " release" files_to_copy = [ From 78acbac2f3eacd3a8b54bb97371d5bb44359b9d1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 5 Jan 2022 10:45:21 +0100 Subject: [PATCH 358/528] Add Cython/3.0a5 build dependency for CHERAB/1.3.0 --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 8 +-- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 8 +-- .../c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb | 54 +++++++++++++++++++ 3 files changed, 62 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb index bb77bca7706..9a080037a64 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index c0847561d7d..f80768c2593 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..08933e60927 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +# Thomas Hoffmann, EMBL Heidelberg: Adapted to v0.29.22, GCCcore 10.2.0 +# 2021/03 +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0a5' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['22060abe55a55a59096982f3e81de2dc8f28c29917d20fa5182f49c4530e27ec'] + +builddependencies = [('binutils', '2.35')] + +# Can't use multi_dep because EBPYTHONPREFIXES are not loaded in order. +# This results in not beeing able to choose Cython version in multi_dep. +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' From 320f7d81b8d3072564382a44a8177ab9ecca26d7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 11:19:08 +0100 Subject: [PATCH 359/528] fix formatting of STRUMPACK-6.1.0-foss-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index a47c361c4c5..d6c33b40db7 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -26,21 +26,21 @@ dependencies = [ configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From b695c7619a7d1855a8293a30515c16830882e96f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 12:52:27 +0200 Subject: [PATCH 360/528] adding easyconfigs: AutoDock-4.2.6-GCC-10.3.0.eb --- .../a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..76a1698a199 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'AutoDock' +version = '4.2.6' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'source_urls': ['https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10'], + 'sources': ['autodocksuite-%(version)s-src.tar.gz'], + 'checksums': ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'], + 'start_dir': 'src/%(namelower)s', +} + +components = [ + ('AutoGrid', version), + ('AutoDock', version), +] + +sanity_check_paths = { + 'files': ['bin/autodock4', 'bin/autogrid4'], + 'dirs': [] +} + +sanity_check_commands = [ + ('autodock4', '--help'), + ('autogrid4', '--help'), +] + +moduleclass = 'tools' From c622cf8dd3fbf4ec118a91303ed1278b972f10d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 11:59:45 +0100 Subject: [PATCH 361/528] adding easyconfigs: VCFtools-0.1.16-GCC-11.2.0.eb --- .../v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb new file mode 100644 index 00000000000..3580f5818bf --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('HTSlib', '1.14'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From be2a36e4ce49ec4d455f33b7ddd3d615ed048beb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 12:32:07 +0100 Subject: [PATCH 362/528] adding easyconfigs: ORCA-5.0.2-gompi-2021b.eb, ORCA-5.0.2-gompi-2021b-static.eb --- .../o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb | 33 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.2-gompi-2021b.eb | 23 +++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb new file mode 100644 index 00000000000..81475b93b99 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb @@ -0,0 +1,33 @@ +name = 'ORCA' +version = '5.0.2' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 4)] +checksums = [ + # orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz + '7623ae43a7d02a36f890a3826e0d021d634addb8e1b2598feb7f9b29d8a3f935', + # orca_5_0_2_linux_x86-64_openmpi411_part2.tar.xz + '905b427a721554a0037986494473a91daa4a0b182dcfbb92fe5d2abccc68df2c', + # orca_5_0_2_linux_x86-64_openmpi411_part3.tar.xz + 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', +] + +# The 5.0.2-static tarballs have redundant top-level directory names names that +# need to be stripped away. +unpack_options = '--strip-components=1' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb new file mode 100644 index 00000000000..8256a206991 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_2_linux_x86-64_shared_openmpi411.tar.xz + '3a26a1a5fbc69e7dca0192237b5e16b69886df31751ae59f7396461428aeee96', +] + +moduleclass = 'chem' From efa7e2a4a93992477c5f4a169dd737247dc291fb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:25:36 +0100 Subject: [PATCH 363/528] adding easyconfigs: Java-15.0.1.eb, Java-15.eb --- easybuild/easyconfigs/j/Java/Java-15.0.1.eb | 15 +++++++++++++++ easybuild/easyconfigs/j/Java/Java-15.eb | 14 ++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-15.0.1.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-15.eb diff --git a/easybuild/easyconfigs/j/Java/Java-15.0.1.eb b/easybuild/easyconfigs/j/Java/Java-15.0.1.eb new file mode 100644 index 00000000000..bb6dfec4233 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-15.0.1.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '15.0.1' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] +checksums = ['83ec3a7b1649a6b31e021cde1e58ab447b07fb8173489f27f427e731c89ed84a'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-15.eb b/easybuild/easyconfigs/j/Java/Java-15.eb new file mode 100644 index 00000000000..78c52a44db6 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-15.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '15' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.1')] + +moduleclass = 'lang' From dd0a4e1b5837ef10e798b90930bfb345f7342e5f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:30:27 +0100 Subject: [PATCH 364/528] adding easyconfigs: Java-17.0.1.eb, Java-17.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 23 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-17.eb | 14 +++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.1.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-17.eb diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb new file mode 100644 index 00000000000..1853440db2c --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -0,0 +1,23 @@ +name = 'Java' +version = '17.0.1' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' + +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +sources = [local_tarball_tmpl % '%(jdkarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + '1c0a73cbb863aad579b967316bf17673b8f98a9bb938602a140ba2e5c38f880a', + local_tarball_tmpl % 'aarch64': + '86653d48787e5a1c029df10da7808194fe8bd931ddd72ff3d42850bf1afb317e', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb new file mode 100644 index 00000000000..e4651cf9c6f --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '17' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.1')] + +moduleclass = 'lang' From 20185a06016c76e291ca374a4ed906b293349621 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 14:32:01 +0100 Subject: [PATCH 365/528] adding easyconfigs: BWA-0.7.17-GCCcore-11.2.0.eb --- .../b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..625b0fff96a --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +moduleclass = 'bio' From 5a6725d5bf7e5b63dbbf93a3316520eb10b7b19a Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 14:32:29 +0100 Subject: [PATCH 366/528] adding easyconfigs: CD-HIT-4.8.1-GCCcore-11.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d99cc6a786d --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'https://github.com/weizhongli/cdhit' +description = """CD-HIT is a very widely used program for clustering and +comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.34.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From 1511b6f07088bc010f82b58c4597fb2ceae50642 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:32:30 +0100 Subject: [PATCH 367/528] update easyconfig: Java-17.0.1.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb index 1853440db2c..9fa9e3e0450 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' -source_urls = ['https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/9/GPL/'] sources = [local_tarball_tmpl % '%(jdkarch)s'] checksums = [ { From b73e3624d686a2bb326987a726f45a333dde5b7b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:33:20 +0100 Subject: [PATCH 368/528] update easyconfig: Java-17.0.1.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb index 9fa9e3e0450..b32ffe92e25 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' -source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/9/GPL/'] +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/12/GPL/'] sources = [local_tarball_tmpl % '%(jdkarch)s'] checksums = [ { From 3db0d9384ddb4384e6a53549e4ebe2755cb72dc3 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 15:16:29 +0100 Subject: [PATCH 369/528] fixed toolchain to GCC --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..bae1e383e4c --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'https://github.com/weizhongli/cdhit' +description = """CD-HIT is a very widely used program for clustering and +comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.34.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From 7f48665ad5d604773f86d03f8c5a3a5adc43ee6f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:25:08 +0100 Subject: [PATCH 370/528] fix formatting of STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 47b5368522d..f5abbb782b6 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -25,23 +25,23 @@ dependencies = [ ] configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From 79745a01576b46333875ead9f59397816940a8d9 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 15:39:40 +0100 Subject: [PATCH 371/528] Added binutils dependency --- .../easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb index bae1e383e4c..d1f7dfd2cb6 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -5,9 +5,9 @@ easyblock = 'MakeCp' name = 'CD-HIT' version = '4.8.1' -homepage = 'https://github.com/weizhongli/cdhit' -description = """CD-HIT is a very widely used program for clustering and -comparing protein or nucleotide sequences.""" +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'openmp': True} @@ -17,7 +17,8 @@ sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] dependencies = [ - ('Perl', '5.34.0'), + ('binutils', '2.37'), + ('Perl', '5.32.1'), ('zlib', '1.2.11'), ] @@ -37,4 +38,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + moduleclass = 'bio' From 6caeaea883f979946826bc64feb1d61b918daa31 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:12 +0100 Subject: [PATCH 372/528] remove whitespace in STRUMPACK-6.1.0-foss-2020b.eb --- easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index d6c33b40db7..7dd06980ec6 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -40,7 +40,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From b5692067ce1ada6071476e328ad29b2598c164c3 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 5 Jan 2022 15:41:33 +0100 Subject: [PATCH 373/528] Java 15 instead of 13 Update easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb Once Java 15 is accepted, this one can use it Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 92bf8614231..7eb4e38d14c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -40,6 +40,6 @@ builddependencies = [ prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " configopts = "--host_jvm_args=--illegal-access=debug" -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '15', '', True)] moduleclass = 'devel' From 7403d93236b3d196002c171fdabdb596d2ceb478 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:37 +0100 Subject: [PATCH 374/528] remove whitespace in STRUMPACK-6.1.0-intel-2020b.eb --- .../easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index f5abbb782b6..4f358cbc2f3 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -41,7 +41,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From 889fa11760bd48d3a1dbcb28d16a9d6113b3c182 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 5 Jan 2022 15:56:43 +0100 Subject: [PATCH 375/528] Delete CD-HIT-4.8.1-GCCcore-11.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb deleted file mode 100644 index d99cc6a786d..00000000000 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'MakeCp' - -name = 'CD-HIT' -version = '4.8.1' - -homepage = 'https://github.com/weizhongli/cdhit' -description = """CD-HIT is a very widely used program for clustering and -comparing protein or nucleotide sequences.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] -sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] -checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] - -dependencies = [ - ('Perl', '5.34.0'), - ('zlib', '1.2.11'), -] - -# make sure compilation flags are passed down (e.g. to enable OpenMP) -buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' - -# put here the list of generated executables when compiling -local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] - -# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] - -fix_perl_shebang_for = ['bin/*.pl'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_list_of_executables], - 'dirs': [], -} - -moduleclass = 'bio' From 4e4a2afc9d631382105faf7775144e8ab3334332 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 16:00:37 +0100 Subject: [PATCH 376/528] Removed changes from last commit + fixed Perl version --- easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb index d1f7dfd2cb6..6b5b72e0ff7 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -17,8 +17,7 @@ sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] dependencies = [ - ('binutils', '2.37'), - ('Perl', '5.32.1'), + ('Perl', '5.34.0'), ('zlib', '1.2.11'), ] From b8f01e5ff9a5a5e589549f81e1ca09c2379a101f Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 16:38:26 +0100 Subject: [PATCH 377/528] adding easyconfigs: BLAST+-2.11.0-gompi-2021b.eb --- .../b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb new file mode 100644 index 00000000000..90b1b862289 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb @@ -0,0 +1,56 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.11.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.77.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), +] + + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From e4350d6bfed68957b03a5a748f9c3be4d31cadc1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Jan 2022 12:40:53 +0200 Subject: [PATCH 378/528] adding easyconfigs: AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb --- ...toDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..90e04c1f06b --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-GPU' +version = '1.5.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ccsb-scripps/AutoDock-GPU' +description = """OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly +parallelizable LGA by processing ligand-receptor poses in parallel over +multiple compute units. +AutoDock is a suite of automated docking tools. It is designed to predict how +small molecules, such as substrates or drug candidates, bind to a receptor of +known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), +] + +parallel = 1 + +# Default CUDA compute capabilities (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '6.1', '7.0'] +# put CUDA compute capabilities in a shell variable to strip dots in make command +prebuildopts = 'CUDA_CC_TARGETS="%(cuda_cc_space_sep)s"; ' + +# Use complation flags from EB +prebuildopts += "sed -i 's/^LFLAGS=.*/LFLAGS=$(LDFLAGS)/;s/^CFLAGS=.*/CFLAGS+=$(IFLAGS) $(LFLAGS)/' Makefile.Cuda && " + +prebuildopts += 'GPU_INCLUDE_PATH=$EBROOTCUDA/include ' +prebuildopts += 'GPU_LIBRARY_PATH=$EBROOTCUDA/lib ' + +# build for CUDA with defined CUDA compute capabilities +buildopts = 'DEVICE=CUDA TARGETS="${CUDA_CC_TARGETS//./}"' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['doc', 'examples', 'LICENSE', 'LICENSE_LGPL', 'README.md'], 'share'), + (['input'], 'share/examples'), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s autodock_gpu_64wi autodock_gpu", +] + +sanity_check_paths = { + 'files': ['bin/autodock_gpu', 'bin/autodock_gpu_64wi', 'bin/adgpu_analysis'], + 'dirs': ['share'], +} + +sanity_check_commands = [('autodock_gpu', '--help')] + +moduleclass = 'tools' From fb90160850bade7a3180160f0a845fc8abca7fc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 6 Jan 2022 15:43:10 +0100 Subject: [PATCH 379/528] adding easyconfigs: STAR-2.7.9a-GCC-11.2.0.eb --- .../s/STAR/STAR-2.7.9a-GCC-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb new file mode 100644 index 00000000000..f43ea1e30a6 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.9a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ff52c9d6daaa9fb7261efa3aa49ef6ce5262aa089b0762a3cbc751e81321050e'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' %(name)s && make %(name)slong' + +parallel = 1 + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +moduleclass = 'bio' From 942b59942b4d897fa38a7225b40c2a8ccd5c8fdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 6 Jan 2022 15:55:22 +0100 Subject: [PATCH 380/528] adding easyconfigs: Subread-2.0.3-GCC-11.2.0.eb --- .../s/Subread/Subread-2.0.3-GCC-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..df58b302599 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.3' + +# HTTPS is not valid +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = ['56cef3a2f914d432713069d5c282f48831c3a1ecc89432ad5580caa322a5f56b'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 509da5f6ae535afe4e42cb3c4b6ddc34c46f396f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Jan 2022 17:16:32 +0200 Subject: [PATCH 381/528] rename and update AutoDock-Vina v1.1.2 and v1.2.3 --- .../AutoDock-Vina-1.1.2-linux_x86.eb} | 11 ++-- .../AutoDock-Vina-1.2.3-GCC-10.3.0.eb | 36 +++++++++++ ...Dock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb | 63 +++++++++++++++++++ 3 files changed, 105 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/a/{AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb => AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb} (59%) create mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb similarity index 59% rename from easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb rename to easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb index 01717004821..d0c0d56d246 100644 --- a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb @@ -5,21 +5,22 @@ easyblock = "Tarball" -name = 'AutoDock_Vina' +name = 'AutoDock-Vina' version = '1.1.2' -versionsuffix = '_linux_x86' +versionsuffix = '-linux_x86' homepage = 'http://vina.scripps.edu/index.html' description = """ AutoDock Vina is an open-source program for doing molecular docking. """ toolchain = SYSTEM -source_urls = ['http://vina.scripps.edu/download/'] -sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.', '_'), versionsuffix)] +source_urls = ['https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12'] +sources = ['autodock_vina_%s%s.tgz' % (version.replace('.', '_'), versionsuffix.replace('-', '_'))] +checksums = ['70543bd953626cf45c53bd1f15ee41e481bde0f94e9746a6be59eabc2cc6bcce'] sanity_check_paths = { 'files': ["bin/vina_split", "bin/vina"], - 'dirs': [] + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..0c3d105812c --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-Vina' +version = '1.2.3' + +homepage = 'https://vina.scripps.edu/' +description = "AutoDock Vina is an open-source program for doing molecular docking." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] + +dependencies = [ + ('Boost', '1.76.0'), +] + +start_dir = 'build/linux/release' + +buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' + +files_to_copy = [ + (['vina', 'vina_split'], 'bin'), + (['docs', 'example', 'LICENSE', 'README.md'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/vina', 'bin/vina_split'], + 'dirs': ['share'], +} + +sanity_check_commands = [('vina', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..bf7713a55fa --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-Vina' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://vina.scripps.edu/' +description = "AutoDock Vina is an open-source program for doing molecular docking." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] + +builddependencies = [ + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +start_dir = 'build/linux/release' + +buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' + +files_to_copy = [ + (['vina', 'vina_split'], 'bin'), + (['docs', 'example', 'LICENSE', 'README.md'], 'share'), +] + +exts_defaultclass = 'PythonPackage' + +# fix hardcoded paths in setup.py +_ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') +_ext_fix_paths = 'sed -i "s|= locate_boost()|= \\\"%s\\\", \\\"%s\\\"|" setup.py && ' % _ext_boost_paths +_ext_fix_paths += "sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name + +exts_list = [ + ('vina', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'], + 'start_dir': 'build/python', + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': _ext_fix_paths, + }), +] + +sanity_check_paths = { + 'files': ['bin/vina', 'bin/vina_split'], + 'dirs': ['share'], +} + +sanity_check_commands = [('vina', '--help')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' From 53489bbd3a108d1cbf43397c04f2fc2464371f14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 7 Jan 2022 09:19:17 +0100 Subject: [PATCH 382/528] adding easyconfigs: DIAMOND-2.0.13-GCC-11.2.0.eb --- .../d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb new file mode 100644 index 00000000000..e9d2b4684fe --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.13' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b79c3a01913999dfa2543f4dd7a3494397a8723ea587207c14683b24e57eac1'] + +builddependencies = [('CMake', '3.21.1')] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From 31b006602d11e29c0282b315a96fdf380e316f8a Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 7 Jan 2022 11:16:53 +0100 Subject: [PATCH 383/528] Add ELSI-RCI-0.1.0 for foss/2021a, foss/2021b, intel/2021a and intel/2021b. --- .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb | 40 ++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb | 40 ++++++++++++++++++ 4 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb new file mode 100644 index 00000000000..8346e384dec --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb new file mode 100644 index 00000000000..02237e1a5b3 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb new file mode 100644 index 00000000000..51095f7a406 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb new file mode 100644 index 00000000000..1f59de009da --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From 3675d444f36c83d8bffbb4598664f82acd67d831 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 7 Jan 2022 11:50:31 +0100 Subject: [PATCH 384/528] Add PSolver-1.8.3 and futile-1.8.3 for foss/2021a, foss/2021b, intel/2021a, and intel/2021b. --- .../f/futile/futile-1.8.3-foss-2021a.eb | 37 +++++++++++++++++ .../f/futile/futile-1.8.3-foss-2021b.eb | 41 +++++++++++++++++++ .../f/futile/futile-1.8.3-intel-2021a.eb | 41 +++++++++++++++++++ .../f/futile/futile-1.8.3-intel-2021b.eb | 41 +++++++++++++++++++ .../f/futile/futile_index_bug.patch | 21 ++++++++++ .../p/PSolver/PSolver-1.8.3-foss-2021a.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-foss-2021b.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-intel-2021a.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-intel-2021b.eb | 38 +++++++++++++++++ 9 files changed, 333 insertions(+) create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb create mode 100644 easybuild/easyconfigs/f/futile/futile_index_bug.patch create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb new file mode 100644 index 00000000000..a684f70cf94 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb new file mode 100644 index 00000000000..0ef7202fe22 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_index_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb new file mode 100644 index 00000000000..dd385e85152 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb new file mode 100644 index 00000000000..d0c0c3be36b --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile_index_bug.patch b/easybuild/easyconfigs/f/futile/futile_index_bug.patch new file mode 100644 index 00000000000..f7649622add --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile_index_bug.patch @@ -0,0 +1,21 @@ +Patch to fix the redefinition of an index variable caught by GCC 11. +author: Micael Oliveira (Max Planck Institute for the Structure and Dynamics of Matter) +diff -rup futile-1.8.3.orig/flib/f_input_file.f90 futile-1.8.3/flib/f_input_file.f90 +--- futile-1.8.3.orig/flib/f_input_file.f90 2018-12-13 10:27:01.000000000 +0100 ++++ futile-1.8.3/flib/f_input_file.f90 2022-01-07 11:35:42.036739693 +0100 +@@ -172,7 +172,6 @@ contains + type(dictionary), pointer :: dict + character(len = *), intent(in) :: file, key + +- integer :: i + type(dictionary), pointer :: ref,iter + character(len = max_field_length) :: val, profile_ + double precision, dimension(2) :: rg +@@ -366,6 +365,7 @@ contains + character(max_field_length), dimension(:), allocatable :: keys + double precision :: var + integer :: dlen, skeys ++ integer :: i + + if (associated(dict%child)) then + if (dict_len(dict) >= 1) then diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb new file mode 100644 index 00000000000..0f0b9fd1313 --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb new file mode 100644 index 00000000000..9cfcdd477ce --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb new file mode 100644 index 00000000000..d4e348ef4fb --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb new file mode 100644 index 00000000000..f87fa8bf98e --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' From 0e0be8a49c408e36528fd868985c00ec13d19269 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:33:07 +0200 Subject: [PATCH 385/528] remove AutoDock-Vina-1.2.3-GCC-10.3.0.eb --- .../AutoDock-Vina-1.2.3-GCC-10.3.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb deleted file mode 100644 index 0c3d105812c..00000000000 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'AutoDock-Vina' -version = '1.2.3' - -homepage = 'https://vina.scripps.edu/' -description = "AutoDock Vina is an open-source program for doing molecular docking." - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -github_account = 'ccsb-scripps' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] - -dependencies = [ - ('Boost', '1.76.0'), -] - -start_dir = 'build/linux/release' - -buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' - -files_to_copy = [ - (['vina', 'vina_split'], 'bin'), - (['docs', 'example', 'LICENSE', 'README.md'], 'share'), -] - -sanity_check_paths = { - 'files': ['bin/vina', 'bin/vina_split'], - 'dirs': ['share'], -} - -sanity_check_commands = [('vina', '--help')] - -moduleclass = 'tools' From 65674c206b9dd6caf7acf85f2bc430668b9d51cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:34:24 +0200 Subject: [PATCH 386/528] remove versionsuffix from AutoDock-Vina v1.2.3 --- ...thon-3.9.5.eb => AutoDock-Vina-1.2.3-foss-2021a.eb} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/a/AutoDock-Vina/{AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb => AutoDock-Vina-1.2.3-foss-2021a.eb} (92%) diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb similarity index 92% rename from easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb index bf7713a55fa..c5f03706a72 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'MakeCp' name = 'AutoDock-Vina' version = '1.2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://vina.scripps.edu/' description = "AutoDock Vina is an open-source program for doing molecular docking." @@ -34,6 +33,11 @@ files_to_copy = [ ] exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} # fix hardcoded paths in setup.py _ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') @@ -45,8 +49,6 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'checksums': ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'], 'start_dir': 'build/python', - 'use_pip': True, - 'sanity_pip_check': True, 'preinstallopts': _ext_fix_paths, }), ] @@ -60,4 +62,4 @@ sanity_check_commands = [('vina', '--help')] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -moduleclass = 'tools' +moduleclass = 'bio' From d48fdae429fff1249d8d867848e2fd1a807bce20 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:46:41 +0200 Subject: [PATCH 387/528] fix codestyle in AutoDock-Vina v1.2.3 --- .../a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb index c5f03706a72..4b2755dce8d 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb @@ -33,7 +33,7 @@ files_to_copy = [ ] exts_defaultclass = 'PythonPackage' -exts_default_options = { +exts_default_options = { 'download_dep_fail': True, 'use_pip': True, 'sanity_pip_check': True, From 68cae9a0667ccadbc9bcd81017a6a79bffa60988 Mon Sep 17 00:00:00 2001 From: MaximeVdB Date: Fri, 7 Jan 2022 16:46:20 +0100 Subject: [PATCH 388/528] adding easyconfigs gengetopt-2.23-GCCcore-10.3.0.eb, openCARP-8.2-foss-2021a.eb and patches: openCARP-8.2_build-info.patch --- .../gengetopt-2.23-GCCcore-10.3.0.eb | 27 +++++++ .../o/openCARP/openCARP-8.2-foss-2021a.eb | 38 ++++++++++ .../o/openCARP/openCARP-8.2_build-info.patch | 72 +++++++++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch diff --git a/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..10ee38c02ba --- /dev/null +++ b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'gengetopt' +version = '2.23' + +homepage = 'https://www.gnu.org/software/gengetopt/gengetopt.html' +description = "Gengetopt is a tool to write command line option parsing code for C programs." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('makeinfo', '6.7', '-minimal'), +] + +sanity_check_paths = { + 'files': ['bin/gengetopt'], + 'dirs': ['share'], +} + +sanity_check_commands = ["gengetopt --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb b/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb new file mode 100644 index 00000000000..77f898e60c5 --- /dev/null +++ b/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMakeCp' + +name = 'openCARP' +version = '8.2' + +homepage = 'https://opencarp.org' +description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/'] +sources = ['openCARP-v%(version)s.tar.gz'] +patches = ['openCARP-8.2_build-info.patch'] +checksums = [ + '56263c4280787c5c7b2ddb2b5f5b5091745dbc7e25d16118071ba0110bff494a', # openCARP-v8.2.tar.gz + '23c8754c749acc5f0f58ac3780ef7e202cefbcc8092e02e832ac2ff540367365', # openCARP-8.2_build-info.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('gengetopt', '2.23'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PETSc', '3.15.1'), + ('zlib', '1.2.11'), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch b/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch new file mode 100644 index 00000000000..c6aaf5d2f46 --- /dev/null +++ b/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch @@ -0,0 +1,72 @@ +avoid having to build from cloned Git repository by adding simulator/build_info.h file, +which was generated using "PETSC_DIR=/foo make build_info.h" in Git repo that corresponds with openCARP v8.2 sources +author: Kenneth Hoste (HPC-UGent) +update to v8.2: Maxime Van den Bossche (HPC-KULeuven) +--- openCARP-v8.2.orig/simulator/CMakeLists.txt 2022-01-06 10:41:19.549302000 +0100 ++++ openCARP-v8.2/simulator/CMakeLists.txt 2022-01-06 10:53:36.486316000 +0100 +@@ -3,13 +3,6 @@ + + ####################################################################### + find_package (Python) + +-add_custom_command(OUTPUT "build_info.h" +- COMMAND Python::Interpreter +- ${CMAKE_CURRENT_SOURCE_DIR}/build_info.py +- DEPENDS build_info.py +- COMMENT "Generate a C header file defining some information about the build" +- VERBATIM +-) + + set(CARP_FILES "openCARP_d.h" "openCARP_p.cc" "openCARP_p.h") + add_custom_command(OUTPUT ${CARP_FILES} +--- openCARP-v8.2.orig/simulator/build_info.h 1970-01-01 01:00:00.000000000 +0100 ++++ openCARP-v8.2/simulator/build_info.h 2022-01-06 10:53:36.486316000 +0100 +@@ -0,0 +1,13 @@ ++#ifndef __BUILD_INFO__ ++#define __BUILD_INFO__ ++ ++#define GIT_COMMIT_TAG "v8.2" ++#define GIT_COMMIT_HASH "dbfd16fdd472375694190b4c7802c0bfba114146" ++#define GIT_COMMIT_COUNT 1257 ++#define GIT_PATH "https://git.opencarp.org/openCARP/openCARP.git" ++ ++#define SUBREPO_REVISIONS "" ++ ++#define SUBREPO_COMMITS "" ++ ++#endif +--- openCARP-v8.2.orig/simulator/build_info.py 2022-01-06 10:41:19.549302000 +0100 ++++ openCARP-v8.2/simulator/build_info.py 2022-01-06 10:53:36.486316000 +0100 +@@ -157,25 +157,13 @@ + """ + + def generate(): +- +- info = git(os.path.dirname(os.path.abspath(__file__))) +- +- # Get subrepo info +- repo_versions = [] +- repo_commits = [] +- +- # we currently have no sub-repos. still, we leave the mechanism in here for later +- +- # repo_versions.append(('slimfem', git('../fem/slimfem')['revision'])) +- # repo_commits.append(( 'slimfem', git('../fem/slimfem')['commit'])) +- +- info['subrepo'] = ','.join(['{0[0]}={0[1]}'.format(v) for v in repo_versions]) +- +- # Assemble commit hashes / revisions +- newline = '," \\\n' + ' ' * 24 + '"' +- info['subrepocommit'] = newline.join(['{0[0]}={0[1]}'.format(v) for v in repo_commits]) +- +- return TEMPLATE.format(**info) ++ return TEMPLATE.format(tag='v8.2', ++ commit='dbfd16fdd472375694190b4c7802c0bfba114146', ++ revision=1257, ++ url='https://git.opencarp.org/openCARP/openCARP.git', ++ subrepo='', ++ subrepocommit='', ++ ) + + def print_build_info(filename): + """ From 3fd719a5debcd1937dee0f145f741d466bcbc771 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 7 Jan 2022 16:57:47 +0100 Subject: [PATCH 389/528] Applied requested changes --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb index 625b0fff96a..5a1898f43db 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -28,18 +28,23 @@ description = """ """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] builddependencies = [ + ('Perl', '5.34.0'), ('binutils', '2.37'), ] dependencies = [('zlib', '1.2.11')] -buildopts = 'CFLAGS="$CFLAGS -fcommon"' +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " moduleclass = 'bio' From e4c27466aa308e87a786f3e956a4e4a464b8497c Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 7 Jan 2022 18:23:41 +0100 Subject: [PATCH 390/528] Applied requested changes --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb index 90b1b862289..b6ec9feea95 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb @@ -21,6 +21,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm sequences of different proteins or the nucleotides of DNA sequences.""" toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] From b7a93983e2de78ce0362732a18b3f0ccb8ee5da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 20:46:42 +0100 Subject: [PATCH 391/528] adding easyconfigs: SHTns-3.5.1-foss-2021b.eb --- .../s/SHTns/SHTns-3.5.1-foss-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb new file mode 100644 index 00000000000..d5ca8e5309e --- /dev/null +++ b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'SHTns' +version = '3.5.1' + +homepage = 'https://bitbucket.org/nschaeff/shtns' +description = """Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical +geometries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/nschaeff/shtns/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['77f8a33b94df8786d2ce9b95cbfbe548f00443625b310b8c64012b22c8a7394f'] + +sanity_check_paths = { + 'files': ['include/shtns_cuda.h', 'include/shtns.f', 'include/shtns.f03', 'include/shtns.h', 'lib/libshtns.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 88ab8a49ccb8b5d227aa0f2f90b9e1d2633c856b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 20:47:12 +0100 Subject: [PATCH 392/528] adding easyconfigs: SHTns-2.7-foss-2021b.eb --- .../s/SHTns/SHTns-2.7-foss-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb new file mode 100644 index 00000000000..12e800cbc5e --- /dev/null +++ b/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'SHTns' +version = '2.7' + +homepage = 'https://bitbucket.org/nschaeff/shtns' +description = """Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical +geometries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/nschaeff/shtns/get/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['725d0aedb26cdceed3a080d1c5f44a746eccba5d8943574fe08faeae370a5ba9'] + +sanity_check_paths = { + 'files': ['include/shtns.f', 'include/shtns.h', 'lib/libshtns.a'], + 'dirs': [], +} + +moduleclass = 'lib' From b5ae8f8a1ade9e1dba969d118e354beb1729f5aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 21:07:20 +0100 Subject: [PATCH 393/528] add ExomeDepth extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index fa5e23bd4c8..2725d3a7c9f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1075,6 +1075,9 @@ exts_list = [ ('M3Drop', '1.20.0', { 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From e3e8f61903843d1de01b8deba5392ef9956a5d0a Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 14:26:07 +0100 Subject: [PATCH 394/528] add corrected Pint and georges --- .../georges-2019.2-foss-2021a-Python-3.9.5.eb | 46 ------------------- .../Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb | 28 ----------- 2 files changed, 74 deletions(-) delete mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb delete mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 8e5f7b94288..00000000000 --- a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'georges' -version = '2019.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ULB-Metronu/georges' -description = """Georges the lemur opinionated particle accelerator modeling Python package. -Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('LMfit', '1.0.3'), - ('matplotlib', '3.4.2'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('m2r', '0.2.1', { - 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], - }), - ('pyDOE', '0.3.8', { - 'modulename': '%(name)s', - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], - 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], - }), -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb deleted file mode 100644 index e695e3bff9f..00000000000 --- a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pint' -version = '0.17' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/hgrecco/pint' -description = """Pint is a Python package to define, operate and -manipulate physical quantities: the product of a numerical value and a -unit of measurement. It allows arithmetic operations between them and -conversions from and to different units.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f4d0caa713239e6847a7c6eefe2427358566451fe56497d533f21fb590a3f313'] - -builddependencies = [('binutils', '2.36.1')] - -dependencies = [ - ('Python', '3.9.5'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'numlib' From 2d5507f40b98a3e5524dcede32a6d2a3905aa888 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 14:57:35 +0100 Subject: [PATCH 395/528] Corrected georges --- .../g/georges/georges-2019.2-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb new file mode 100644 index 00000000000..983cbb100ce --- /dev/null +++ b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'georges' +version = '2019.2' + +homepage = 'https://github.com/ULB-Metronu/georges' +description = """Georges the lemur opinionated particle accelerator modeling Python package. +Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('LMfit', '1.0.3'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('m2r', '0.2.1', { + 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], + 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], + }), +] + +moduleclass = 'phys' From caafa9f56eb32b38ef457c53abfd6783dc4d3afd Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 15:22:50 +0100 Subject: [PATCH 396/528] Corrected zgoubi --- easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 3ca79813105..3e393662461 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -9,6 +9,10 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('GCC', '10.3.0'), +] + source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] sources = ['%(version)s/zgoubi-%(version)s.tar.bz2'] checksums = ['0b0f3d28496edbf7be868c24b0c927b7f1bc88cc29df9c235d9b28dc933489e0'] From d98971e7a933dd1fcb627cc5a88046f854350a2b Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 15:45:47 +0100 Subject: [PATCH 397/528] Corrected zgoubi ver2 --- easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 3e393662461..72f3866d7b2 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -10,7 +10,7 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ - ('GCC', '10.3.0'), + ('GCCcore', '10.3.0'), ] source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] From 4b738d20103f8337ee8b473c75fa08259f2639a2 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 16:29:31 +0100 Subject: [PATCH 398/528] Corrected zgoubi ver3, corrected arrow, boost-histogram --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 3 +-- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 7 +++---- .../easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 425e7dbb2d6..44d1e6242b7 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -28,12 +28,11 @@ dependencies = [ ('Boost', '1.76.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 5a0bffca63f..72364a1f7c9 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -1,11 +1,10 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'boost_histogram' version = '1.2.1' -homepage = 'https://pypi.org/project/boost-histogram/' -description = """This is one of the fastest libraries for histogramming, -while still providing the power of a full histogram object""" +homepage = 'https://boost-histogram.readthedocs.io' +description = """Boost-histogram is a Python package providing Python bindings for Boost.Histogram.""" toolchain = {'name': 'foss', 'version': '2021a'} diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 72f3866d7b2..bfa771d6eef 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -10,7 +10,7 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ - ('GCCcore', '10.3.0'), + ('binutils', '2.36.1'), ] source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] @@ -22,7 +22,7 @@ prebuildopts += "sed -i '/guide/d' Makefile &&" buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' -files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin')] +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop', 'exemples/exemples/'], 'bin')] sanity_check_paths = { 'files': ["bin/zgoubi", "bin/zpop"], From ddd179d92f4d231fcb67230a0a1f377eacce8f10 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 18:25:01 +0100 Subject: [PATCH 399/528] Updated boost-histogram --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 72364a1f7c9..dc1266f3590 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -17,6 +17,8 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = None + exts_list = [ (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', From 6a70ff2b0f1c57706c0c418671515f65f8b4ac68 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 19:26:28 +0100 Subject: [PATCH 400/528] Updated boost-histogram ver2 --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index dc1266f3590..9f5d02ee0c5 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = None +download_dep_fail = True exts_list = [ (name, version, { From b0bdcc76625c8cb068c62bc5e793ee415e362888 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 22:40:50 +0100 Subject: [PATCH 401/528] Corrected Arrow and boost-histogram --- .../easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 2 +- .../boost_histogram-1.2.1-foss-2021a.eb | 15 +++++++++------ 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 44d1e6242b7..026891935f0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -30,7 +30,7 @@ dependencies = [ start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 9f5d02ee0c5..89eac2ddd7a 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -8,6 +8,9 @@ description = """Boost-histogram is a Python package providing Python bindings f toolchain = {'name': 'foss', 'version': '2021a'} +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'] + dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), @@ -19,11 +22,11 @@ sanity_pip_check = True download_dep_fail = True -exts_list = [ - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], - }), -] +#exts_list = [ +# (name, version, { +# 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', +# 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], +# }), +#] moduleclass = 'math' From 565e6901c4faf820ab3aa80085aa2ad837e4d0bf Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 23:00:22 +0100 Subject: [PATCH 402/528] Corrected boost-histogram v2 --- .../boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 89eac2ddd7a..51d4dea9124 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -20,13 +20,4 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True - -#exts_list = [ -# (name, version, { -# 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', -# 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], -# }), -#] - moduleclass = 'math' From 0e5eb7365a748829be6a4baadd4a2eb37c230be0 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sun, 9 Jan 2022 09:07:45 +0100 Subject: [PATCH 403/528] Corrected boost-histogram v2 --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 51d4dea9124..2f723340824 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True + sanity_pip_check = True moduleclass = 'math' From b12221a04510f8ba0e451bfa5e03c42a0c5c1cd8 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sun, 9 Jan 2022 11:33:09 +0100 Subject: [PATCH 404/528] Corrected boost-histogram v3 and zgoubi --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 ++ easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 2f723340824..8c6ffcd8688 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -21,4 +21,6 @@ use_pip = True sanity_pip_check = True +download_dep_fail = True + moduleclass = 'math' diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index bfa771d6eef..f330d78d088 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -22,7 +22,8 @@ prebuildopts += "sed -i '/guide/d' Makefile &&" buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' -files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop', 'exemples/exemples/'], 'bin')] +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin'), 'exemples'] +postinstallcmds = ["mv %(installdir)s/exemples %(installdir)s/examples"] sanity_check_paths = { 'files': ["bin/zgoubi", "bin/zpop"], From 17ab59cc9902d09ecc249cc6d17b22df6b9be987 Mon Sep 17 00:00:00 2001 From: Jonney Huang Date: Mon, 10 Jan 2022 04:17:10 +1300 Subject: [PATCH 405/528] Update easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb update dependencies Co-authored-by: Alex Domingo --- .../easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 4b5db8af46f..202a2598490 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -9,7 +9,12 @@ description = """ A distributed storage benchmark for files, objects & blocks wi toolchain = {'name': 'GCC', 'version': '10.3.0'} -dependencies = [('Boost', '1.76.0'), ('libaio', '0.3.112')] +dependencies = [ + ('Boost', '1.76.0'), + ('libaio', '0.3.112'), + ('numactl', '2.0.14'), + ('ncurses', '6.2'), +] sources = [{ 'filename': "v%(version)s.tar.gz", From b76ddebcb2a794dd86cdb04ce8684c2dbd775f9b Mon Sep 17 00:00:00 2001 From: easybuild Date: Sun, 9 Jan 2022 15:24:33 +0000 Subject: [PATCH 406/528] udpate base on feedback --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 202a2598490..905272ac462 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -16,22 +16,17 @@ dependencies = [ ('ncurses', '6.2'), ] -sources = [{ - 'filename': "v%(version)s.tar.gz", - 'git_config': { - 'url': 'https://github.com/breuner', - 'repo_name': 'elbencho', - 'tag': 'v%(version)s' - }, - -}] +github_account = 'breuner' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] files_to_copy = ["bin"] sanity_check_paths = { - 'dirs': files_to_copy, 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], + 'dirs': [], } +buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' moduleclass = 'tools' From 575a2525b1528ea2483a01ba016f5062d02c3ff1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Jan 2022 09:37:56 +0100 Subject: [PATCH 407/528] rename patch files required for building Bazel 3.7.2 with GCCcore/11.2.0 + Java/15 --- .../b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 31 +++++++------------ .../b/Bazel/Bazel-3.7.2_fix-GCC-11.patch | 22 +++++++++++++ ...15.patch => Bazel-3.7.2_fix-Java-15.patch} | 0 .../b/Bazel/gcc11-2-bazel-3.7.2.patch | 10 ------ .../b/Bazel/gcc11-bazel-3.7.2.patch | 10 ------ 5 files changed, 33 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch rename easybuild/easyconfigs/b/Bazel/{java15.patch => Bazel-3.7.2_fix-Java-15.patch} (100%) delete mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch delete mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 7eb4e38d14c..a694933bb18 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -7,29 +7,20 @@ It is used to build the majority of Google's software.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [ - 'https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] patches = [ - '%(name)s-3.4.1-fix-grpc-protoc.patch', - 'java15.patch', - '%(name)s-3.7.1_fix-protobuf-env.patch', - 'gcc11-bazel-3.7.2.patch', - 'gcc11-2-bazel-3.7.2.patch', - + 'Bazel-3.4.1-fix-grpc-protoc.patch', + 'Bazel-3.7.1_fix-protobuf-env.patch', + 'Bazel-3.7.2_fix-GCC-11.patch', + 'Bazel-3.7.2_fix-Java-15.patch', ] checksums = [ - # bazel-3.7.2-dist.zip - 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', - # Bazel-3.4.1-fix-grpc-protoc.patch - 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', - '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # java15.patch - # Bazel-3.7.1_fix-protobuf-env.patch - '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', - # gcc11-bazel-3.7.2.patch - '32dc4abdc45bfcf70e9d93a66150b89646c801f8704930f0b713038366e40d40', - # gcc11-2-bazel-3.7.2.patch - '3160caff050330e33df1f7afb649e8303bf4af969ef7722639bd0f3c3ae036b4', + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # bazel-3.7.2-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch + '7fd5846f2ed1f27af9528a900f284f95ad982f3e7d486264c3bdee890a9c22fb', # Bazel-3.7.2_fix-GCC-11.patch + '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # Bazel-3.7.2_fix-Java-15.patch ] builddependencies = [ @@ -37,9 +28,9 @@ builddependencies = [ ('Python', '3.9.6'), ('Zip', '3.0'), ] +dependencies = [('Java', '15', '', True)] prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " configopts = "--host_jvm_args=--illegal-access=debug" -dependencies = [('Java', '15', '', True)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch new file mode 100644 index 00000000000..6f1575c39c2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch @@ -0,0 +1,22 @@ +add missing include statements to fix compilation with GCC 11.x +author: Alexandre Strube (JSC) +--- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 ++++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 +@@ -16,6 +16,7 @@ + #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ + + #include ++#include + + #include "third_party/ijar/common.h" + +--- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 ++++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 +@@ -16,6 +16,7 @@ + #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H + + #include "third_party/ijar/common.h" ++#include + + namespace devtools_ijar { + diff --git a/easybuild/easyconfigs/b/Bazel/java15.patch b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-Java-15.patch similarity index 100% rename from easybuild/easyconfigs/b/Bazel/java15.patch rename to easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-Java-15.patch diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch deleted file mode 100644 index c7ceaa84318..00000000000 --- a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 -+++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 -@@ -16,6 +16,7 @@ - #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H - - #include "third_party/ijar/common.h" -+#include - - namespace devtools_ijar { - diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch deleted file mode 100644 index b46eda73836..00000000000 --- a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 -+++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 -@@ -16,6 +16,7 @@ - #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ - - #include -+#include - - #include "third_party/ijar/common.h" - From 1cf035d82f59db47d1d90b4553d1430bd718b93f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 09:43:00 +0100 Subject: [PATCH 408/528] Remove spurious empty lines. --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb | 1 - easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb index 8346e384dec..98126fbf976 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb @@ -24,7 +24,6 @@ builddependencies = [ ('CMake', '3.20.1'), ] - # Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb index 02237e1a5b3..55420c821fa 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb @@ -24,7 +24,6 @@ builddependencies = [ ('CMake', '3.21.1'), ] - # Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", From b5c1ac74e475d572423985b01bc220a1ac02dba5 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 10:24:32 +0100 Subject: [PATCH 409/528] Add ParMETIS for gompi/2021a, gompi/2021b, iimpi/2021a, and iimpi/2021b. --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb | 29 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb | 29 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb | 25 ++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb | 25 ++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb new file mode 100644 index 00000000000..50d82a6369e --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.20.1')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb new file mode 100644 index 00000000000..8451916f797 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.21.1')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb new file mode 100644 index 00000000000..d044ec9b5d2 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.20.1')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb new file mode 100644 index 00000000000..b0299fdf5c7 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.21.1')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From f16b62e6c09be2bcb9d2487b7a7791ab05271598 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 11:03:07 +0100 Subject: [PATCH 410/528] Move ELSI-RCI to GCC and intel-compilers toolchains, as it only require BLAS/LAPACK for running tests, which in any case are broken. --- ...I-RCI-0.1.0-foss-2021a.eb => ELSI-RCI-0.1.0-GCC-10.3.0.eb} | 4 ++-- ...I-RCI-0.1.0-foss-2021b.eb => ELSI-RCI-0.1.0-GCC-11.2.0.eb} | 4 ++-- ...el-2021a.eb => ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb} | 4 ++-- ...el-2021b.eb => ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb} | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-foss-2021a.eb => ELSI-RCI-0.1.0-GCC-10.3.0.eb} (92%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-foss-2021b.eb => ELSI-RCI-0.1.0-GCC-11.2.0.eb} (92%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-intel-2021a.eb => ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb} (91%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-intel-2021b.eb => ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb} (91%) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb index 98126fbf976..7cfd4db094e 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb similarity index 92% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb index 55420c821fa..69dcafbd651 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb similarity index 91% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb index 51095f7a406..7f403973ffd 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb similarity index 91% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb index 1f59de009da..829899b7d3f 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] From eedbd16487054ca50c2b0bc9616cd3d8591b920c Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 11:58:41 +0100 Subject: [PATCH 411/528] Moved Perl dependency to run-time rependencies --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb index 5a1898f43db..e9730661d4c 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -34,13 +34,13 @@ source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] -builddependencies = [ +builddependencies = [('binutils', '2.37')] + +dependencies = [ ('Perl', '5.34.0'), - ('binutils', '2.37'), + ('zlib', '1.2.11'), ] -dependencies = [('zlib', '1.2.11')] - # Allow use of x86 intrinsics on PPC prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " From b60f11fd4df32f296524af6cb775b3d06c8a5020 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 12:11:17 +0100 Subject: [PATCH 412/528] Updated the version of BLAST --- ...ST+-2.11.0-gompi-2021b.eb => BLAST+-2.12.0-gompi-2021b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/BLAST+/{BLAST+-2.11.0-gompi-2021b.eb => BLAST+-2.12.0-gompi-2021b.eb} (94%) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb similarity index 94% rename from easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb index b6ec9feea95..eb841a154fe 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'BLAST+' -version = '2.11.0' +version = '2.12.0' homepage = 'https://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -25,7 +25,7 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] +checksums = ['fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88'] dependencies = [ ('zlib', '1.2.11'), From c45992b9428dbc1359590946a13268c2e5007c4b Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 13:09:49 +0100 Subject: [PATCH 413/528] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-11.2.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b1fd926ac8b --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From f605291e1a0e8d9c0ee4ebf5bcf4165533c3d448 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 13:48:27 +0100 Subject: [PATCH 414/528] adding easyconfigs: CheckM-1.1.3-foss-2021b.eb, HMMER-3.3.2-gompi-2021b.eb --- .../c/CheckM/CheckM-1.1.3-foss-2021b.eb | 65 +++++++++++++++ .../h/HMMER/HMMER-3.3.2-gompi-2021b.eb | 79 +++++++++++++++++++ 2 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb new file mode 100644 index 00000000000..c1bc07048f5 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb @@ -0,0 +1,65 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# Updated by: Filip Kružík (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'CheckM' +version = '1.1.3' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://pypi.python.org/packages/source/c/checkm-genome', + 'https://data.ace.uq.edu.au/public/CheckM_databases/', +] +sources = [ + 'checkm-genome-%(version)s.tar.gz', + { + 'filename': 'checkm_data_2015_01_16.tar.gz', + 'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s", + }, +] +checksums = [ + '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644', # checkm-genome-1.1.3.tar.gz + '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz +] + +# Dependencies: +# https://github.com/Ecogenomics/CheckM/blob/master/setup.py +dependencies = [ + ('Python', '3.9.6'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2021.10'), # numpy + ('matplotlib', '3.4.3'), + ('Pysam', '0.17.0'), + ('DendroPy', '4.5.2'), +] + +download_dep_fail = True +use_pip = True + +# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm +postinstallcmds = [ + "cp -a %(builddir)s/data %(installdir)s", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "%(installdir)s/bin/checkm data setRoot %(installdir)s/data", +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb new file mode 100644 index 00000000000..5f8c0591214 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb @@ -0,0 +1,79 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] + +builddependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 9f554aad069522cfc5ce4990dee327399a3084b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Jan 2022 15:44:38 +0100 Subject: [PATCH 415/528] enable tests for Bazel 3.7.2 with GCCcore/11.2.0 + remove configopts/prebuildopts that are not required --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index a694933bb18..53603c713d1 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [('Java', '15', '', True)] -prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " -configopts = "--host_jvm_args=--illegal-access=debug" +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." moduleclass = 'devel' From 4a63114ae0456d1de32ab47b9fb1d93878fb151b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 10 Jan 2022 15:48:43 +0100 Subject: [PATCH 416/528] Update Bazel-3.7.2-GCCcore-11.2.0.eb --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 53603c713d1..b4db72bd13c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -28,6 +28,8 @@ builddependencies = [ ('Python', '3.9.6'), ('Zip', '3.0'), ] + +configopts = "--host_jvm_args=--illegal-access=debug" dependencies = [('Java', '15', '', True)] runtest = True From 251973c5428b44bf4d16fb9a840d2afcf6b5639b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 10 Jan 2022 16:52:32 +0100 Subject: [PATCH 417/528] Update Bazel-3.7.2-GCCcore-11.2.0.eb --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index b4db72bd13c..d0148e063b5 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,6 @@ builddependencies = [ ('Zip', '3.0'), ] -configopts = "--host_jvm_args=--illegal-access=debug" dependencies = [('Java', '15', '', True)] runtest = True From 05c41036b6d29e9fed96d802fec85da87399ef48 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Tue, 11 Jan 2022 14:15:05 +0200 Subject: [PATCH 418/528] adding easyconfigs: hivtrace-0.6.2-foss-2021a.eb --- .../h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb new file mode 100644 index 00000000000..9137968d933 --- /dev/null +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonBundle' + +name = 'hivtrace' +version = '0.6.2' + +homepage = 'https://github.com/veg/hivtrace' +description = """HIV-TRACE is an application that identifies potential transmission clusters within a + supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('tn93', '1.0.7'), + ('cURL', '7.76.0'), + ('Pysam', '0.16.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hyphy-python', '0.1.10', { + 'modulename': 'HyPhy', + 'source_urls': ['https://pypi.python.org/packages/source/h/hyphy-python'], + 'checksums': ['b83f7e890c0c21b301c1c761967bd6328df9fad972653888b02baad71055c186'], + }), + ('fakemp', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/fakemp'], + 'checksums': ['320885d5851e0c568cd4247fa81e48f055e435822643e5bda9d82edc53c3b938'], + }), + ('hppy', '0.9.9', { + 'source_urls': ['https://pypi.python.org/packages/source/h/hppy'], + 'checksums': ['9112acc888c51c14a88669f084a7ebf39fa62bdd47924a1e3cee6824cfbc4610'], + }), + ('tornado', '6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('bioext', '0.19.9', { + 'modulename': 'BioExt', + 'source_urls': ['https://pypi.python.org/packages/source/b/bioext'], + 'checksums': ['bada8d7e83928a8c934e1e482bc945f43a3234c6c4ea3afcef7fa34c0ea610a3'], + }), + ('hivclustering', '1.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/h/hivclustering'], + 'checksums': ['673fa81b6b44ae7a7bfa32897bc01c26cfe807052aadc3d1f5a729b0df3a335f'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hivtrace'], + 'checksums': ['f4aabd2bbc326aecb9ab22de8f6877628f908cfa8eee458feb06d48bb19425e6'], + }), +] + +# This two files come bundled compressed but the software expects them uncompressed +postinstallcmds = [ + 'gunzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/hivtrace/rsrc/LANL.FASTA.gz', + 'gunzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/hivtrace/rsrc/LANL.TN93OUTPUT.csv.gz', +] + +sanity_check_paths = { + 'files': ['bin/hivtrace'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From d6d87ead2c0dafc2b22e18a789fefde8e23ecf3d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 11 Jan 2022 16:21:16 +0100 Subject: [PATCH 419/528] Removed reference to DUNE_PY_DIR environment variable --- .../easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 2 -- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 3c4f56daebe..966f23ed47c 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -7,8 +7,6 @@ homepage = "https://www.dune-project.org/groups/core/" description = """The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 6d875c7c146..e838e7272a0 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -9,8 +9,6 @@ the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} From 8848db55f97855a1f64b2393b017ab80ce8768bb Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:37:06 +0100 Subject: [PATCH 420/528] adding easyconfigs: SPAdes-3.15.3-GCC-11.2.0.eb --- .../s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..047f59e56a7 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute +# Updated by: +# Filip Kružík (INUITS) + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.3' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b2e5a9fd7a65aee5ab886222d6af4f7b7bc7f755da7a03941571fabd6b9e1499'] + +builddependencies = [ + ('CMake', '3.22.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' From 2511223f0f6fea58c6423f140b023d252dc26c0e Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:39:09 +0100 Subject: [PATCH 421/528] adding easyconfigs: RDP-Classifier-2.13-Java-17.0.1.eb --- .../RDP-Classifier-2.13-Java-17.0.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb new file mode 100644 index 00000000000..223cfba95ba --- /dev/null +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'RDP-Classifier' +version = '2.13' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://sourceforge.net/projects/rdp-classifier' +description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic + assignments from domain to genus, with confidence estimates for each assignment.""" + +toolchain = SYSTEM + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['rdp_classifier_%(version)s.zip'] +checksums = ['d2eb9a989d7e31ff824de6876bc1d8ab70d97112ece167afe8d87a3cd412086a'] + +dependencies = [('Java', '17.0.1')] + +modextrapaths = { + 'CLASSPATH': 'dist/classifier.jar', + 'RDP_JAR_PATH': 'dist/classifier.jar', +} + +sanity_check_paths = { + 'files': ['dist/classifier.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From f25b13916c9fba26b78c67bc6154869b2aadedfd Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:40:22 +0100 Subject: [PATCH 422/528] adding easyconfigs: PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb --- .../PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb new file mode 100644 index 00000000000..814735de515 --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb @@ -0,0 +1,97 @@ +# author: Denis Kristak + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] +checksums = ['9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f'] + +dependencies = [ + ('Perl', '5.34.0'), + ('cairo', '1.16.0'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.8001', { + 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['673c4387e7896c1a216099c1fbb3faaa7763d7f5f95a1a56a60a2a2906c131c5'], + }), + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('Pod::Usage', '2.0', { + 'source_tmpl': 'Pod-Usage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['530943a9ac3ba00404d7be8ee8572f30f6db9de123cd725af3647333a87d4fea'], + }), + ('Cairo', '1.109', { + 'source_tmpl': 'Cairo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['8219736e401c2311da5f515775de43fd87e6384b504da36a192f2b217643077f'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + 'checksums': ['f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('Math::Cephes::Matrix', '0.5305', { + 'source_tmpl': 'Math-Cephes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1'], + }), + ('Math::MatrixReal', '2.13', { + 'source_tmpl': 'Math-MatrixReal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + 'checksums': ['4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2'], + }), + ('Text::SimpleTable', '2.07', { + 'source_tmpl': 'Text-SimpleTable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + 'checksums': ['256d3f38764e96333158b14ab18257b92f3155c60d658cafb80389f72f4619ed'], + }), + ('Contextual::Return', '0.2.1', { + 'source_tmpl': 'Contextual-Return-v%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + 'checksums': ['17a1ed1043a2abe123920894d6023709e834de66ef766be86e4cfbb96b1dd16c'], + }), +] + +fix_perl_shebang_for = ["*.pl"] + +postinstallcmds = ["chmod +x %(installdir)s/*.pl"] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From adbc0f4a945648b2cafd2ada40a77ec8be953a97 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:53:19 +0100 Subject: [PATCH 423/528] adding easyconfigs: MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb --- .../MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..2c4859be86e --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.14'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' From 06ff5cb3408def06bcaab0a46027ed845f297f95 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:54:51 +0100 Subject: [PATCH 424/528] adding easyconfigs: CompareM-0.1.2-foss-2021b-Python-3.9.6.eb --- .../CompareM-0.1.2-foss-2021b-Python-3.9.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..c4b519eba6c --- /dev/null +++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'CompareM' +version = '0.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dparks1134/CompareM' +description = "A toolbox for comparative genomics." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), +] + +use_pip = True + +exts_list = [ + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('biolib', '0.1.9', { + 'checksums': ['bc9ae68c6d76d46e4295fe0b1df5a48b575fe96374bd96d624c3330feb94856f'], + }), + ('comparem', version, { + 'checksums': ['bdfd3db957b151f6bdf711203d65bfda7209c5b46c5ce275da5bce2b4d490afa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/comparem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["comparem -h"] + +sanity_pip_check = True + +moduleclass = 'bio' From b87055761e309b34c0616f901576cb1782f8b1db Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:57:17 +0100 Subject: [PATCH 425/528] adding easyconfigs: AMOS-3.1.0-foss-2021b.eb, MUMmer-4.0.0beta2-GCCcore-11.2.0.eb --- .../a/AMOS/AMOS-3.1.0-foss-2021b.eb | 44 +++++++++++++++++++ .../MUMmer-4.0.0beta2-GCCcore-11.2.0.eb | 36 +++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..cba3aad0459 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'AMOS' +version = '3.1.0' + +homepage = 'http://amos.sourceforge.net' +description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'cstd': 'c++98'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AMOS-%(version)s_GCC-4.7.patch'] +checksums = [ + '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz + '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch +] + +dependencies = [ + ('expat', '2.4.1'), + ('MUMmer', '4.0.0beta2'), +] + +sanity_check_paths = { + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} + +parallel = 1 # make crashes otherwise + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5e7cd6bc7cc --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0beta2' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From ac646d9b2db3978054603b0e874391216f3b5f12 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:30:29 +0100 Subject: [PATCH 426/528] adding easyconfigs: MinPath-1.6-intel-2021b-Python-3.9.6.eb and patches: MinPath-1.6_fix-glpsol-path.patch --- .../MinPath-1.6-intel-2021b-Python-3.9.6.eb | 49 +++++++++++++++++++ .../MinPath/MinPath-1.6_fix-glpsol-path.patch | 18 +++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..60338744ce1 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [{ + 'filename': 'minpath%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/mgtools/', + 'repo_name': 'MinPath', + 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', + }, +}] +checksums = ['8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db'] + +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] + +dependencies = [ + ('Python', '3.9.6'), + ('GLPK', '5.0'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] + +sanity_check_paths = { + 'files': ['MinPath.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "python3 MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "python3 MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +modextravars = {'MinPath': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch new file mode 100644 index 00000000000..ab00b150df8 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch @@ -0,0 +1,18 @@ +--- MinPath-1.6_fix-glpsol-path.py 2022-01-11 19:05:58.000000000 +0100 ++++ MinPath.py 2022-01-11 20:43:56.981520000 +0100 +@@ -20,13 +20,14 @@ + import math + + minpath = os.path.dirname(os.path.abspath(sys.argv[0])) ++glpkroot = os.getenv("EBROOTGLPK") + print("minpath directory: " + minpath) + if not os.path.exists(minpath + "/data"): + minpath = os.environ.get('MinPath') + if not (os.path.exists(minpath) and os.path.exists(minpath + "/data")): + sys.exit("Environment variable MinPath not set") + +-keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", minpath + "/glpk-4.6/examples/glpsol" ++keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", glpkroot + "/bin/glpsol" + + def intmatrix(dim1, dim2): + mat = [] From a2a1efa36eeccbfc9361dbe6602e026b1e263efc Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:34:10 +0100 Subject: [PATCH 427/528] Removed pyver from version suffix --- ...5-gompi-2021b-Python-3.9.6.eb => MetaBAT-2.15-gompi-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/m/MetaBAT/{MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb => MetaBAT-2.15-gompi-2021b.eb} (96%) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb similarity index 96% rename from easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 2c4859be86e..3a2f07771f6 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'MetaBAT' version = '2.15' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://bitbucket.org/berkeleylab/metabat' description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" From 31524763e7c68ac05ceb0b4f2e1d273195fb6510 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:36:28 +0100 Subject: [PATCH 428/528] Removed pyver from version suffix --- ...2-foss-2021b-Python-3.9.6.eb => CompareM-0.1.2-foss-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/c/CompareM/{CompareM-0.1.2-foss-2021b-Python-3.9.6.eb => CompareM-0.1.2-foss-2021b.eb} (96%) diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb similarity index 96% rename from easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb index c4b519eba6c..29fffcda612 100644 --- a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'CompareM' version = '0.1.2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/dparks1134/CompareM' description = "A toolbox for comparative genomics." From 4c9e7f49daa006c7537837018196e62b87eca484 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:39:17 +0100 Subject: [PATCH 429/528] Removed pyver from version suffix --- ....6-intel-2021b-Python-3.9.6.eb => MinPath-1.6-intel-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/m/MinPath/{MinPath-1.6-intel-2021b-Python-3.9.6.eb => MinPath-1.6-intel-2021b.eb} (97%) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb similarity index 97% rename from easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 60338744ce1..7e9da621bb6 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'Tarball' name = 'MinPath' version = '1.6' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://omics.informatics.indiana.edu/MinPath' description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions From c993ec87db2a7aec1f5d17182b6656d795da2776 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 11 Jan 2022 21:43:04 +0100 Subject: [PATCH 430/528] use Java version 17 --- ...ifier-2.13-Java-17.0.1.eb => RDP-Classifier-2.13-Java-17.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/r/RDP-Classifier/{RDP-Classifier-2.13-Java-17.0.1.eb => RDP-Classifier-2.13-Java-17.eb} (95%) diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb similarity index 95% rename from easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb rename to easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb index 223cfba95ba..2150bc84025 100644 --- a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['rdp_classifier_%(version)s.zip'] checksums = ['d2eb9a989d7e31ff824de6876bc1d8ab70d97112ece167afe8d87a3cd412086a'] -dependencies = [('Java', '17.0.1')] +dependencies = [('Java', '17')] modextrapaths = { 'CLASSPATH': 'dist/classifier.jar', From 38dd9a2d086df87b3a14d79c39cde834bcf62be2 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 22:11:45 +0100 Subject: [PATCH 431/528] Fixed checksums --- easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 7e9da621bb6..f3ab1349538 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -18,9 +18,11 @@ sources = [{ 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', }, }] -checksums = ['8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db'] - patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db', # minpath1.6.tar.gz + '4bf2c9ca9cb67ab4d5751b0af85df73c5cd7e368fc54737bab0907ce5a06a640', # MinPath-1.6_fix-glpsol-path.patch +] dependencies = [ ('Python', '3.9.6'), From 0964c080e8f4f0c816ef12809ad2784dd12d9d8a Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 23:10:17 +0100 Subject: [PATCH 432/528] adding easyconfigs: FragGeneScan-1.31-GCCcore-11.2.0.eb, IDBA-UD-1.1.3-GCC-11.2.0.eb, MaxBin-2.2.7-gompi-2021b.eb --- .../FragGeneScan-1.31-GCCcore-11.2.0.eb | 38 ++++++++++++++ .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb | 49 +++++++++++++++++++ .../m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb | 40 +++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ad2ea72a080 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [("Perl", "5.34.0")] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..8d4d05d6460 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb new file mode 100644 index 00000000000..db60c60fedb --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('Bowtie2', '2.4.4'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 608d5d86b0de3b0f69851d17fca159632a5c0b2d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 12 Jan 2022 09:21:42 +0100 Subject: [PATCH 433/528] Moved builddependencies before dependencies as requested by code review in pull request (both configs) --- .../d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 10 +++++----- .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 966f23ed47c..b6aae99f163 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -11,6 +11,11 @@ These modules build the foundation for higher-level components. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -20,11 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('portalocker', '2.3.2', { 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index e838e7272a0..52e3809d42a 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -13,6 +13,11 @@ components of DUNE-FEM and the DUNE core modules to Python. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -25,11 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('fenics-ufl', '2019.1.0', { 'modulename': 'ufl', From 04f1219964f73be279a43a76a48c3884dc3eca2e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 12 Jan 2022 18:47:27 +0100 Subject: [PATCH 434/528] change versionsuffix to -linux-x64 --- .../{Blender-3.0.0-binary.eb => Blender-3.0.0-linux-x64.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/Blender/{Blender-3.0.0-binary.eb => Blender-3.0.0-linux-x64.eb} (96%) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb similarity index 96% rename from easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb rename to easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb index 8de30bc9841..0d0c2f24298 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb @@ -5,7 +5,7 @@ easyblock = 'PackedBinary' name = 'Blender' version = '3.0.0' -versionsuffix = '-binary' +versionsuffix = '-linux-x64' homepage = 'https://www.blender.org' description = """ From 1d890ab869cb0213435a50d71a86c3edc95f269a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 10:50:41 +0100 Subject: [PATCH 435/528] adding easyconfigs: Python-2.7.18-GCCcore-11.2.0.eb --- .../p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 422 ++++++++++++++++++ 1 file changed, 422 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c569dc49d45 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -0,0 +1,422 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.36'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.2'), # required for cryptography + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 8 January 2022, to the most recent versions still supporting Python 2.x +exts_list = [ + ('setuptools', '44.1.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('wheel', '0.37.1', { + 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + }), + ('pip', '20.3.4', { + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.8.0', { + 'checksums': ['672d8ebee84921862110f23fcec2acea191ef58543d34dfe9ef3d9f13c31cddf'], + }), + ('Cython', '0.29.26', { + 'checksums': ['af377d543a762867da11fcf6e558f7a4a535ff8693f30cce123fab10c00fa312'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.17.0', { + 'checksums': ['b9f500bb439e4153d0330610f5d26baaf18d17b8ced1bc54410d189385ea68aa'], + }), + ('enum34', '1.1.10', { + 'modulename': 'enum', + 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.0', { + 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + }), + ('cryptography', '3.3.2', { + 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.9.1', { + 'checksums': ['a1fdded3b55f61d23389e4fe52d9ae428960ac958d2edf50373faa5d8926edd0'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '3.0.5', { + 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], + }), + ('pytz', '2021.3', { + 'checksums': ['acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326'], + }), + ('bitstring', '3.1.9', { + 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.4', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579'], + }), + ('filelock', '3.2.1', { + 'checksums': ['9cdd29c411ab196cf4c35a1da684f7b9da723696cb356efa45bf5eb1ff313ee3'], + }), + ('importlib_resources', '3.3.1', { + 'checksums': ['0ed250dbd291947d1a298e89f39afcc477d5a6624770503034b72588601bcc05'], + }), + ('platformdirs', '2.0.2', { + 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], + }), + ('virtualenv', '20.13.0', { + 'checksums': ['d8458cf8d59d0ea495ad9b34c2599487f8a7772d796f9910858376d1600dd2dd'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '4.0.0', { + 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], + }), + ('certifi', '2021.10.8', { + 'checksums': ['78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872'], + }), + ('urllib3', '1.26.8', { + 'checksums': ['0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c'], + }), + ('requests', '2.27.1', { + 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.6', { + 'checksums': ['7d8bcb5555003cdf4a8d2872c538faa3a0f5d20630cb360e518ca3b981795e5f'], + }), + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + ('configparser', '4.0.2', { + 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], + }), + ('contextlib2', '0.6.0.post1', { + 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], + }), + ('importlib_metadata', '1.7.0', { + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '5.0.0', { + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '21.4.0', { + 'modulename': 'attr', + 'checksums': ['626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd'], + }), + ('backports.functools-lru-cache', '1.6.4', { + 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('pytest', '4.6.11', { + 'checksums': ['50fa82392f2120cc3ec2ca0a75ee615be4c479e66669789771f1758332be4353'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.3', { + 'checksums': ['a6d58433de0ae800347cab1fa3043cebbabe8baa9d29e668f1c768cb87a333c6'], + }), + ('packaging', '20.9', { + 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], + }), + ('sphinxcontrib-websupport', '1.1.2', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.3.0', { + 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], + }), + ('docutils', '0.17.1', { + 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('Babel', '2.9.1', { + 'checksums': ['bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.10.0.0', { + 'checksums': ['13b4ad211f54ddbf93e5901a9967b1e07720c1d1b78d596ac6a439641aa1b130'], + }), + ('Sphinx', '1.8.6', { + 'checksums': ['e096b1b369dbb0fcb95a31ba8c9e1ae98c588e601f08eada032248e1696de4b1'], + }), + ('sphinx-bootstrap-theme', '0.8.0', { + 'checksums': ['038ee7e89478e064b5dd7e614de6f3f4cec81d9f9efbebb06e105693d6a50924'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.9.0', { + 'checksums': ['869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('singledispatch', '3.7.0', { + 'checksums': ['c1a4d5c1da310c3fd8fccfb8d4e1cb7df076148fd5d858a819e37fffe44f3092'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('functools32', '3.2.3-2', { + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('futures', '3.3.0', { + 'modulename': False, + 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], + }), + ('glob2', '0.6', { + 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('regex', '2021.3.17', { + 'checksums': ['4b8a1fb724904139149a43e172850f35aa6ea97fb0545244dc0b805e0154ed68'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('entrypoints', '0.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19'], + }), + ('SecretStorage', '2.3.1', { + 'modulename': False, # Doesn't work properly under Python2, but is required for keyring + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), + ('tomlkit', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + }), + ('shellingham', '1.4.0', { + 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.16.1', { + 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], + }), + ('pkginfo', '1.8.2', { + 'checksums': ['542e0d0b6750e2e21c20179803e40ab50598d8066d51097a0e382cba9eb02bff'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.7', { + 'modulename': 'poetry.core', + 'checksums': ['98c11c755a16ef6c5673c22ca94a3802a7df4746a0853a70b6fae8b9f5cac206'], + }), + ('poetry', '1.1.12', { + 'checksums': ['5c66e2357fe37b552462a88b7d31bfa2ed8e84172208becd666933c776252567'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From 0f00c16d759199289e0822e4e915c5d618c1a9a8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 10:51:23 +0100 Subject: [PATCH 436/528] adding easyconfigs: OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb --- ...penBabel-3.1.1-gompi-2021a-Python-3.9.5.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..4cb86c42299 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb @@ -0,0 +1,57 @@ +name = 'OpenBabel' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch' +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('Eigen', '3.3.9'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.16.0'), # optional: for .png output + ('Boost', '1.76.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' From 3b564c4e256f0280059397617a2930f0c78be967 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 13 Jan 2022 10:49:19 +0000 Subject: [PATCH 437/528] Add sanity_check_all_components parameter --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index a7982e2cd57..627ddf691a1 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -23,6 +23,7 @@ dependencies = [ ] default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True # Also build and install LAPACKE, which FlexiBLAS does not support yet components = [ @@ -36,15 +37,14 @@ components = [ 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], 'sources': ['v%(version)s.tar.gz'], 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], - 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ - -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ - -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, }), ] -sanity_check_paths = { - 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], - 'dirs': [], -} - moduleclass = 'lib' From 10bfb550ee6e28d822375273434fb70314cada7f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 13 Jan 2022 12:50:29 +0100 Subject: [PATCH 438/528] Adjust versions of extensions to match Python-3.9.6-GCCcore-11.2.0.eb when possible --- .../p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 114 ++++++++++-------- 1 file changed, 61 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index c569dc49d45..baae8b422fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -12,6 +12,10 @@ source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('binutils', '2.37'), ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib @@ -34,14 +38,15 @@ exts_default_options = { } # order is important! -# package versions updated 8 January 2022, to the most recent versions still supporting Python 2.x +# package versions updated 13 January 2022, to the most recent versions still supporting Python 2.x +# while keeping it in sync with the Python 3 version for this toolchain/version exts_list = [ ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('wheel', '0.37.1', { - 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + ('wheel', '0.36.2', { + 'checksums': ['e11eefd162658ea59a60a0f6c7d493a7190ea4b9a85e335b33489d9f17e0245e'], }), ('pip', '20.3.4', { 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], @@ -55,11 +60,11 @@ exts_list = [ ('paycheck', '1.0.2', { 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), - ('pbr', '5.8.0', { - 'checksums': ['672d8ebee84921862110f23fcec2acea191ef58543d34dfe9ef3d9f13c31cddf'], + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], }), - ('Cython', '0.29.26', { - 'checksums': ['af377d543a762867da11fcf6e558f7a4a535ff8693f30cce123fab10c00fa312'], + ('Cython', '0.29.24', { + 'checksums': ['cdf04d07c3600860e8c2ebaad4e8f52ac3feb212453c1764a49ac08c827e8443'], }), ('six', '1.16.0', { 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], @@ -67,8 +72,8 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('setuptools_scm', '4.1.2', { - 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + ('setuptools_scm', '5.0.2', { + 'checksums': ['83a0cedd3449e3946307811a4c7b9d89c4b5fd464a2fb5eeccd0a5bb158ae5c8'], }), ('python-dateutil', '2.8.2', { 'modulename': 'dateutil', @@ -109,13 +114,14 @@ exts_list = [ ('idna', '2.10', { 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], }), - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], }), - ('cffi', '1.15.0', { - 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + ('cffi', '1.14.6', { + 'checksums': ['c9a875ce9d7fe32887784274dd533c57909b7b1dcadcc128a2ac21331a9765dd'], }), ('cryptography', '3.3.2', { + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], }), ('pyasn1', '0.4.8', { @@ -128,8 +134,8 @@ exts_list = [ ('bcrypt', '3.1.7', { 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], }), - ('paramiko', '2.9.1', { - 'checksums': ['a1fdded3b55f61d23389e4fe52d9ae428960ac958d2edf50373faa5d8926edd0'], + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], }), ('pyparsing', '2.4.7', { 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], @@ -146,8 +152,8 @@ exts_list = [ ('mock', '3.0.5', { 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], }), - ('pytz', '2021.3', { - 'checksums': ['acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326'], + ('pytz', '2021.1', { + 'checksums': ['83a4a90894bf38e243cf052c8b58f381bfe9a7a483f6a9cab140bc7f702ac4da'], }), ('bitstring', '3.1.9', { 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], @@ -155,12 +161,12 @@ exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], }), - ('distlib', '0.3.4', { + ('distlib', '0.3.2', { 'source_tmpl': 'distlib-%(version)s.zip', - 'checksums': ['e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579'], + 'checksums': ['106fef6dc37dd8c0e2c0a60d3fca3e77460a48907f335fa28420463a6f799736'], }), - ('filelock', '3.2.1', { - 'checksums': ['9cdd29c411ab196cf4c35a1da684f7b9da723696cb356efa45bf5eb1ff313ee3'], + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], }), ('importlib_resources', '3.3.1', { 'checksums': ['0ed250dbd291947d1a298e89f39afcc477d5a6624770503034b72588601bcc05'], @@ -168,8 +174,11 @@ exts_list = [ ('platformdirs', '2.0.2', { 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], }), - ('virtualenv', '20.13.0', { - 'checksums': ['d8458cf8d59d0ea495ad9b34c2599487f8a7772d796f9910858376d1600dd2dd'], + ('backports.entry_points_selectable', '1.1.1', { + 'checksums': ['914b21a479fde881635f7af5adc7f6e38d6b274be32269070c53b698c60d5386'], + }), + ('virtualenv', '20.7.0', { + 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], }), ('docopt', '0.6.2', { 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], @@ -180,20 +189,20 @@ exts_list = [ ('chardet', '4.0.0', { 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], }), - ('certifi', '2021.10.8', { - 'checksums': ['78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872'], + ('certifi', '2021.5.30', { + 'checksums': ['2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee'], }), - ('urllib3', '1.26.8', { - 'checksums': ['0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c'], + ('urllib3', '1.26.6', { + 'checksums': ['f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f'], }), - ('requests', '2.27.1', { - 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], }), ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py_expression_eval', '0.3.14', { - 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + ('py_expression_eval', '0.3.13', { + 'checksums': ['6e7d59d391d54a034609ce66b820e7dd68c757672d166dcc514bf7abf15ba57e'], }), ('tabulate', '0.8.9', { 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], @@ -204,8 +213,8 @@ exts_list = [ ('atomicwrites', '1.4.0', { 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], }), - ('py', '1.11.0', { - 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + ('py', '1.10.0', { + 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], }), ('scandir', '1.10.0', { 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], @@ -231,12 +240,11 @@ exts_list = [ ('more-itertools', '5.0.0', { 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), - ('attrs', '21.4.0', { + ('attrs', '21.2.0', { 'modulename': 'attr', - 'checksums': ['626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd'], + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -261,14 +269,14 @@ exts_list = [ ('Pygments', '2.5.2', { 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], }), - ('imagesize', '1.3.0', { - 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], }), ('docutils', '0.17.1', { 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], }), - ('snowballstemmer', '2.2.0', { - 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + ('snowballstemmer', '2.1.0', { + 'checksums': ['e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914'], }), ('Babel', '2.9.1', { 'checksums': ['bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0'], @@ -291,8 +299,8 @@ exts_list = [ ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), - ('psutil', '5.9.0', { - 'checksums': ['869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25'], + ('psutil', '5.8.0', { + 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], }), ('future', '0.18.2', { 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], @@ -355,9 +363,9 @@ exts_list = [ 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], }), - ('tomlkit', '0.7.0', { + ('tomlkit', '0.7.2', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + 'checksums': ['173ad840fa5d2aac140528ca1933c29791b79a374a0861a80347f42ec9328117'], }), ('shellingham', '1.4.0', { 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], @@ -368,8 +376,8 @@ exts_list = [ ('pyrsistent', '0.16.1', { 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], }), - ('pkginfo', '1.8.2', { - 'checksums': ['542e0d0b6750e2e21c20179803e40ab50598d8066d51097a0e382cba9eb02bff'], + ('pkginfo', '1.7.1', { + 'checksums': ['e7432f81d08adec7297633191bbf0bd47faf13cd8724c3a13250e51d542635bd'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], @@ -377,8 +385,8 @@ exts_list = [ ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], }), - ('simplejson', '3.17.6', { - 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + ('simplejson', '3.17.3', { + 'checksums': ['da72a452bcf4349fc467a12b54ab0e63e654a571cacc44084826d52bde12b6ee'], }), ('webencodings', '0.5.1', { 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], @@ -406,12 +414,12 @@ exts_list = [ ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), - ('poetry-core', '1.0.7', { + ('poetry-core', '1.0.3', { 'modulename': 'poetry.core', - 'checksums': ['98c11c755a16ef6c5673c22ca94a3802a7df4746a0853a70b6fae8b9f5cac206'], + 'checksums': ['2315c928249fc3207801a81868b64c66273077b26c8d8da465dccf8f488c90c5'], }), - ('poetry', '1.1.12', { - 'checksums': ['5c66e2357fe37b552462a88b7d31bfa2ed8e84172208becd666933c776252567'], + ('poetry', '1.1.7', { + 'checksums': ['3833c7b22411b8393e8e594fede94f0ef7a5260c19f51e272cce76512cffe6c8'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', From f55296948b29cc33edca84fc3f6a645fdabf2ebe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 13:23:57 +0100 Subject: [PATCH 439/528] remove preinstallopts for cryptography 3.3.2, only needed with 3.4.x or newer where Rust is used as a build dependency --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index baae8b422fc..72ceefe329f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -121,7 +121,6 @@ exts_list = [ 'checksums': ['c9a875ce9d7fe32887784274dd533c57909b7b1dcadcc128a2ac21331a9765dd'], }), ('cryptography', '3.3.2', { - 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], }), ('pyasn1', '0.4.8', { From 82efb84217b818be2dff091f006dca645b9b7571 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 13:33:00 +0100 Subject: [PATCH 440/528] The versionsuffix for python 3 was dropped in 2020b onwards --- ...penBabel-3.1.1-gompi-2021a-Python-3.9.5.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb deleted file mode 100644 index 4cb86c42299..00000000000 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,57 +0,0 @@ -name = 'OpenBabel' -version = '3.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many - languages of chemical data. It's an open, collaborative project allowing anyone - to search, convert, analyze, or store data from molecular modeling, chemistry, - solid-state materials, biochemistry, or related areas.""" - -toolchain = {'name': 'gompi', 'version': '2021a'} -# avoid failing tests on skylake and broadwell CPUs. -# remove option 'optarch' when building on CPUs that don't support AVX2 -# see also: https://github.com/openbabel/openbabel/issues/2138 -toolchainopts = {'pic': True, 'optarch': 'mavx2'} - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] -patches = [ - # Fix test failure with Python 3 - # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch' -] -checksums = [ - 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz - '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('SWIG', '4.0.2'), -] -dependencies = [ - ('Python', '3.9.5'), - ('zlib', '1.2.11'), - ('libxml2', '2.9.10'), - ('Eigen', '3.3.9'), - ('RapidJSON', '1.1.0'), - ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.76.0'), # optional: for Maestro formats -] - -configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' -# Enable support for OpenMP compilation of forcefield code (optional) -configopts += '-DENABLE_OPENMP=ON ' - -# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR -# (set in the easyblock) having invalid values. Work around this with some symlinks. -postinstallcmds = [ - 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', - 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', -] - -pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT -runtest = 'test' - -moduleclass = 'chem' From 7ccefee354a3b3cfa4dbb0d5de85d2f07a5b3cd9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 13:49:58 +0100 Subject: [PATCH 441/528] Better without versionsuffix field --- .../OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb new file mode 100644 index 00000000000..e76ffb84b87 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb @@ -0,0 +1,56 @@ +name = 'OpenBabel' +version = '3.1.1' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch' +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('Eigen', '3.3.9'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.16.0'), # optional: for .png output + ('Boost', '1.76.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' From a1b1e372366ef508b417d5ff0e835a4e74c69645 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 15:14:30 +0100 Subject: [PATCH 442/528] Added requested changes --- .../m/MinPath/MinPath-1.6-intel-2021b.eb | 20 ++++++------------- .../MinPath/MinPath-1.6_fix-glpsol-path.patch | 2 ++ 2 files changed, 8 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index f3ab1349538..154cc13b16c 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -2,6 +2,8 @@ easyblock = 'Tarball' name = 'MinPath' version = '1.6' +# no tagged commit for MinPath 1.6, commit was determined based on commit history +local_commit = '46d3e81a4dca2310d558bea970bc002b15d44767' homepage = 'https://omics.informatics.indiana.edu/MinPath' description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions @@ -10,18 +12,12 @@ description = """MinPath (Minimal set of Pathways) is a parsimony approach for b toolchain = {'name': 'intel', 'version': '2021b'} -sources = [{ - 'filename': 'minpath%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/mgtools/', - 'repo_name': 'MinPath', - 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', - }, -}] +source_urls = ['https://github.com/mgtools/MinPath/archive/'], +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] checksums = [ - '8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db', # minpath1.6.tar.gz - '4bf2c9ca9cb67ab4d5751b0af85df73c5cd7e368fc54737bab0907ce5a06a640', # MinPath-1.6_fix-glpsol-path.patch + '57e6b55cd00507578bad7528c60e3ad055311f62db928bd7c8de793513cec5a3', # MinPath-1.6.tar.gz + '117e45c6f35e3c944232dd5dd4789400d44c4b9b733b936adbb548b58e046c4b', # MinPath-1.6_fix-glpsol-path.patch ] dependencies = [ @@ -43,8 +39,4 @@ sanity_check_commands = [ "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", ] -modextrapaths = {'PATH': ''} - -modextravars = {'MinPath': '%(installdir)s'} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch index ab00b150df8..270a34e091a 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch @@ -1,3 +1,5 @@ +Make MinPath use different glpk library than it comes with. +Author: Filip Kružík (INUITS) --- MinPath-1.6_fix-glpsol-path.py 2022-01-11 19:05:58.000000000 +0100 +++ MinPath.py 2022-01-11 20:43:56.981520000 +0100 @@ -20,13 +20,14 @@ From 79c999745949f843ca196f1dcf3e57d30ae87500 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 15:59:06 +0100 Subject: [PATCH 443/528] adding easyconfigs: MACSE-2.06-Java-15.eb --- .../easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb new file mode 100644 index 00000000000..131198b6bf9 --- /dev/null +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -0,0 +1,27 @@ +easyblock = 'JAR' + +name = 'MACSE' +version = '2.06' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://bioweb.supagro.inra.fr/macse/index.php' +description = 'MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.' + +toolchain = SYSTEM + +local_jarname = '%(namelower)s_v%(version)s.jar' + +sources = [local_jarname] +source_urls = ['https://bioweb.supagro.inra.fr/macse/releases/'] + +dependencies = [('Java', '15')] + +modloadmsg = 'To execute %(name)s run: java -jar $EBROOT%(name)s/' + local_jarname + '\n' + +sanity_check_commands = ['java -jar $EBROOTMACSE/' + local_jarname + ' -v'] +sanity_check_paths = { + 'files': [local_jarname], + 'dirs': [] +} + +moduleclass = 'bio' From 2ab4b6472c8fcee742eb347073bf737004013131 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 16:17:39 +0100 Subject: [PATCH 444/528] Split description in to multiple lines --- easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb index 131198b6bf9..f92b5d68ed4 100644 --- a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -5,7 +5,9 @@ version = '2.06' versionsuffix = '-Java-%(javaver)s' homepage = 'https://bioweb.supagro.inra.fr/macse/index.php' -description = 'MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.' +description = '''MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to +contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding +gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure.''' toolchain = SYSTEM From cbb4fb8f509ea05c3c0185c25931832a780b97ee Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 16:25:01 +0100 Subject: [PATCH 445/528] add checksum --- easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb index f92b5d68ed4..665ad19f703 100644 --- a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -13,8 +13,9 @@ toolchain = SYSTEM local_jarname = '%(namelower)s_v%(version)s.jar' -sources = [local_jarname] source_urls = ['https://bioweb.supagro.inra.fr/macse/releases/'] +sources = [local_jarname] +checksums = ['e4f9f0dd443a7147d0f010e9ecd6940aa80f9ec68c687f8ba134209ac1e33398'] dependencies = [('Java', '15')] From 7473ebc0e3a0476c35fea90f382e55880c8303ab Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 16:44:46 +0100 Subject: [PATCH 446/528] adding easyconfigs: DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb, pullseq-1.0.2-GCCcore-11.2.0.eb, Ruby-3.0.1-GCCcore-11.2.0.eb --- ...l-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb | 53 ++++++ .../p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb | 37 ++++ .../r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 164 ++++++++++++++++++ 3 files changed, 254 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb new file mode 100644 index 00000000000..f77c59e946d --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] + +dependencies = [ + ('R', '4.1.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.12.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'modulename': 'DASTool', + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b0676dedca5 --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] +dependencies = [ + ('PCRE', '8.45'), +] + +preconfigopts = "./bootstrap && " + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6e37c235463 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '3.0.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['369825db2199f6aeef16b408df6a04ebaddb664fb9af0ec8c686b0ce7ab77727'] + +builddependencies = [('binutils', '2.37')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2021-07-02 +exts_list = [ + ('ffi', '1.15.3', { + 'checksums': ['98d5c5c4281c9c0466acc60cf0e79124bf3c311417fd97e7473e41722953fbf1'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.5.1', { + 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.21.0', { + 'checksums': ['f9394457cb1dd5ca1b7bdc0dfbbd8f56f5cde40f45f96bc90f0f895a87e41b77'], + }), + ('arr-pm', '0.0.11', { + 'checksums': ['f1ab088421276f446da1971c5071defd1504855ec46e196815fa43cd62d61a9f'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.1.1', { + 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], + }), + ('ruby2_keywords', '0.0.4', { + 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + }), + ('faraday-net_http', '1.0.1', { + 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + }), + ('faraday', '1.3.0', { + 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + }), + ('faraday_middleware', '1.0.0', { + 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.5', { + 'checksums': ['13a8fc3921ce4df8e04fb65f1037251decb08d74757b41163688bd1c1feccd39'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '4.0.6', { + 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], + }), + ('addressable', '2.7.0', { + 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + }), + ('concurrent-ruby', '1.1.9', { + 'checksums': ['0ec0846d991c38f355b4228ad8ea77aa69c3fdaa320cd574dafedc10c4688a5b'], + }), + ('i18n', '1.8.10', { + 'checksums': ['ca24e52fdd6ad7af419241eef8c41e65ef4e3499c6b252df13f697919eb24e3c'], + }), + ('minitest', '5.14.4', { + 'checksums': ['f4716634d71b3ffb627cd63ba4f6f0f77c7a3f17353b1bdf52c8a7f2e0e4e7a7'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.4.2', { + 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + }), + ('activesupport', '5.0.7.2', { + 'checksums': ['f75cc67fb08421bdf4c2a383a47d9b3b02ce5eec4749704b1286fb0c12c98bad'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.14.0', { + 'checksums': ['10e267a39d7e2a92d944e5681ba46dbd211b5b5b6cf9b51afb769b8417247ead'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.4.4', { + 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + }), + ('rspec-support', '3.10.2', { + 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + }), + ('rspec-mocks', '3.10.2', { + 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], + }), + ('rspec-expectations', '3.10.1', { + 'checksums': ['27acf5d5df13f8cc8f7158001ebf572513bcec3d45404ba76e0a8998895ce9eb'], + }), + ('rspec-core', '3.10.1', { + 'checksums': ['ac9abdc9577a3a34e9e92815603da8343931055ab4fba1c2a49de6dd3b749673'], + }), + ('rspec', '3.10.0', { + 'checksums': ['b870b43d49ae4a4e063b94976d2742b0854ec10458c425d569b5556ee5898ab7'], + }), + ('rack', '2.2.3', { + 'checksums': ['2638e7eb6689a5725c7e16f30cc4aa4e31694dc3ca30d790952526781bd0bb44'], + }), + ('rack-protection', '2.1.0', { + 'checksums': ['1f523c16e5b32f139c8f6f1e3b3eb53aaa7a69bc79a30f3e80f8a93c89242a95'], + }), + ('tilt', '2.0.10', { + 'checksums': ['9b664f0e9ae2b500cfa00f9c65c34abc6ff1799cf0034a8c0a0412d520fac866'], + }), + ('mustermann', '1.1.1', { + 'checksums': ['0a21cfe505869cce9ce17998db5260344e78df81ae857c07a62143fd30299531'], + }), + ('sinatra', '2.1.0', { + 'checksums': ['f323e4446f3e2a132dcaaa134f89caddb29dd88370317f4f32faf5797f1ea535'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.2.21', { + 'checksums': ['3c8dc5e0cf66d385a9b33751e54986290d42023c5e1bba2b5df094917b6e234a'], + }), +] + +moduleclass = 'lang' From ed89c21a009b308b6ab561a81521d2843dc7cacc Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 17:27:56 +0100 Subject: [PATCH 447/528] Removed pyver suffix --- .../DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..81cc573725f --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] + +dependencies = [ + ('R', '4.1.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.12.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'modulename': 'DASTool', + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + + +moduleclass = 'bio' From 1a9547795683daf8acb2ede74e3f4af4c40b3926 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 13 Jan 2022 17:28:17 +0100 Subject: [PATCH 448/528] Delete DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb --- ...l-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb deleted file mode 100644 index f77c59e946d..00000000000 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'Tarball' - -name = 'DAS_Tool' -version = '1.1.1' -versionsuffix = '-R-%(rver)s-Python-%(pyver)s' - -homepage = 'https://github.com/cmks/DAS_Tool' -description = """DAS Tool is an automated method that integrates the results of a flexible number of binning - algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] - -dependencies = [ - ('R', '4.1.2'), - ('Python', '3.9.6'), - ('Ruby', '3.0.1'), - ('pullseq', '1.0.2'), - ('prodigal', '2.6.3'), - ('BLAST+', '2.12.0'), -] - -exts_defaultclass = 'RPackage' - -exts_list = [ - (name, version, { - 'source_tmpl': 'DASTool_%(version)s.tar.gz', - 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], - 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], - 'modulename': 'DASTool', - }), -] - -postinstallcmds = [ - "cd %(installdir)s; unzip db.zip", - "chmod a+x %(installdir)s/DAS_Tool", -] - -sanity_check_paths = { - 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], - 'dirs': ['DASTool/R'], -} - -modextrapaths = { - 'PATH': '', - 'R_LIBS_SITE': '', -} - - -moduleclass = 'bio' From 6f85ffb5358d8bbd492db589e7991ddfbf3c5d86 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 18:36:49 +0100 Subject: [PATCH 449/528] adding easyconfigs: Short-Pair-20170125-foss-2021b.eb and patches: Short-Pair-20170125-Python3fix.patch --- .../Short-Pair-20170125-Python3fix.patch | 204 ++++++++++++++++++ .../Short-Pair-20170125-foss-2021b.eb | 47 ++++ 2 files changed, 251 insertions(+) create mode 100644 easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch create mode 100644 easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch new file mode 100644 index 00000000000..4c5da5540cd --- /dev/null +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch @@ -0,0 +1,204 @@ +Makes Short-Pair compatible with Phyton3 +Author: Filip Kružík (INUITS) +--- Short-Pair_fix 2022-01-11 17:08:22.763000000 +0100 ++++ Short-Pair.py 2022-01-11 17:05:28.709307000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python3 + import os + import sys + import pickle +@@ -9,10 +9,12 @@ + from numpy import percentile + from numpy import std + from numpy import mean ++from os.path import abspath, dirname, realpath # Tocado JT + + +-sequence_length_global = 0 + ++sequence_length_global = 0 ++exec_path = abspath(dirname(realpath(__file__))) # Tocado JT + + def get_first_sequence_in_fasta_file(fasta_file): + fi = open(fasta_file, 'rt') +@@ -29,15 +31,16 @@ + + + def step1(fastaFile, pattern): +- command = "DNA2Protein 1-6 %s %s" % (fastaFile, pattern) ++ command = "%s/DNA2Protein 1-6 %s %s" % (exec_path, fastaFile, pattern) # exec_path, FPS + os.system(command) + + def step2(hmm, inputFile): +- inputFileDir = os.path.dirname(inputFile) ++ inputFileDir = abspath(os.path.dirname(inputFile)) ++ inputFile = inputFile.split('/')[-1] + outputDir = os.path.join(inputFileDir, '../out1') + +- outputFile = os.path.join(outputDir, inputFile+'.hmmer') +- command = 'hmmsearch -E 1000 --domtblout %s %s %s' % (outputFile, hmm, inputFile) ++ outputFile = os.path.join(outputDir, inputFile +'.hmmer') ++ command = '%s/../hmmer/hmmsearch -E 1000 --domtblout %s %s %s/%s > /dev/null' % (exec_path, outputFile, hmm, inputFileDir, inputFile) # exec_path, FPS + os.system(command) + return outputFile + +@@ -71,12 +74,12 @@ + + def combineHmmer(inputFolder, outputFolder, allOutput, nDomains, namePattern): + fa = open(allOutput, 'wt') +- for i in xrange(1, nDomains+1): ++ for i in range(1, nDomains+1): + # for i in xrange(201, nDomains+1): + mapLinesList = [] + mapScoresList = [] + readPairSet = set() +- for j in xrange(1, 7): ++ for j in range(1, 7): + inputFile = namePattern % (i, j) + fi = open(inputFolder+'/'+inputFile, 'rt') + mapReadPairToLines = {} +@@ -100,8 +103,8 @@ + outputFile = os.path.join(outputFolder, outputFile) + fo = open(outputFile, 'wt') + for pair in sorted(readPairSet): +- maxScore = -sys.maxint +- for j in xrange(1, 7): ++ maxScore = -sys.maxsize ++ for j in range(1, 7): + mapReadPairToLines = mapLinesList[j-1] + mapReadPairToScore = mapScoresList[j-1] + if pair not in mapReadPairToScore: +@@ -120,7 +123,7 @@ + mapLinesList = [] + mapScoresList = [] + readPairSet = set() +- for j in xrange(1, 7): ++ for j in range(1, 7): + inputFile = namePattern % (j) + fi = open(inputFolder+'/'+inputFile, 'rt') + mapReadPairToLines = {} +@@ -142,8 +145,8 @@ + ### start to combine + fo = open(outputFile, 'wt') + for pair in sorted(readPairSet): +- maxScore = -sys.maxint +- for j in xrange(1, 7): ++ maxScore = -sys.maxsize ++ for j in range(1, 7): + mapReadPairToLines = mapLinesList[j-1] + mapReadPairToScore = mapScoresList[j-1] + if pair not in mapReadPairToScore: +@@ -240,7 +243,7 @@ + f.close() + return hmmList + +-def step7(inputFile): ++def step7(inputFile): + hmmYList = []; hmmNList = [] + hmmList = readHmm(inputFile) + for hmm in hmmList: +@@ -494,7 +497,7 @@ + os.mkdir(outputFolder) + for hmm in sorted(hmmList, key=lambda x:x.name): + family = hmm.name +- command = "get_hmm.sh %s %s > %s/%s.hmm" % (family, hmmFile, outputFolder,family) ++ command = "%s/get_hmm.sh %s %s > %s/%s.hmm" % (exec_path, family, hmmFile, outputFolder,family) # exec_path, FPS + os.system(command) + + def runHmmer(inputFile1, inputFile2, inputFile3, hmmFolder, outputFileInput, fastaPath, faaPath, filterFile): +@@ -530,13 +533,12 @@ + for (read, family, key) in readSet: + readNames.add(read.replace('|','_')) + write = False +- + fi = open(inputFile2, 'rt') + nLine = 0 + for line in fi: + if line[0]=='>': + read = line[1:].strip(); +- read = read.replace("|","_") ++ read = read.replace("|","_") + if read[:-2]+".2" in readNames: + outputFile = r'%s/%s.fasta' % (fastaPath, read) + fo = open(outputFile, 'wt') +@@ -578,18 +580,20 @@ + tmpRead = tmpRead[:-2] + '.1' + fastaFile = r'%s/%s.fasta' % (fastaPath, tmpRead) + faaFile = r'%s/%s.faa' % (faaPath, tmpRead) +- command = "DNA2Protein 1-6 %s %s" % (fastaFile, faaFile) ++ command = "%s/DNA2Protein 1-6 %s %s" % (exec_path, fastaFile, faaFile) # exec_path, FPS + os.system(command) + outputFile = r'%s.allframe' % (faaFile) + fo = open(outputFile, 'wt') +- maxScore = -sys.maxint ++ maxScore = -sys.maxsize + maxString = '' +- for i in xrange(1,7): +- command = "hmmer3_pipeline_missing_end.sh" +- args = [command, "%s/%s.hmm" % (hmmFolder, family), "%s.frame%d" % (faaFile, i), "%d" % i]; +- outString = subprocess.Popen(args, stdout=subprocess.PIPE).communicate()[0] ++ for i in range(1,7): ++ command = "%s/hmmer3_pipeline_missing_end.sh" % exec_path # exec_path, FPS ++ args = [command, "%s/%s.hmm" % (hmmFolder, family), "%s.frame%d" % (faaFile, i), "%d" % i, "10"] ++ my_env = os.environ # Add SQM/bin/hmmer to the PATH env. variable for subprocess ++ my_env['PATH'] = '%s/../hmmer:' % exec_path + os.environ['PATH'] ++ outString = subprocess.Popen(args, env=my_env, stdout=subprocess.PIPE).communicate()[0].decode() + fo.write(outString) +- if outString != '': ++ if outString: + row = outString.split() + score = float(row[2]) + if score > maxScore: +@@ -707,7 +711,7 @@ + mapLengthToFrequency[length] = frequency + total += frequency + fi.close() +- for key in mapLengthToFrequency.keys(): ++ for key in list(mapLengthToFrequency.keys()): + mapLengthToFrequency[key] = mapLengthToFrequency[key] / float(total) + + mapReadToLine = {} +@@ -779,7 +783,7 @@ + fo.close() + + mapNumberToFrequency = {} +- for read in mapReadToFamilySet.keys(): ++ for read in list(mapReadToFamilySet.keys()): + number = len(mapReadToFamilySet[read]) + if number not in mapNumberToFrequency: + mapNumberToFrequency[number] = 0 +@@ -800,11 +804,11 @@ + step1(fastaFile2, pattern2) + step3InputList = [] + step3OutputList = [] +- for i in xrange(1,7): ++ for i in range(1,7): + inputFile = pattern1 + '.frame%d' % i + step2Output = step2(hmm, inputFile) + step3InputList.append(step2Output) +- for i in xrange(1,7): ++ for i in range(1,7): + inputFile = pattern2 + '.frame%d' % i + step2Output = step2(hmm, inputFile) + step3InputList.append(step2Output) +@@ -832,8 +836,8 @@ + step12(hmmFile, hmmList, hmmFolder) + step13OutputFile1 = step11Output+'_1'; step13OutputFile2 = step11Output+'_2' + workingDir = os.path.dirname(step11Output) +- fastaPath = '%s/fasta' % workingDir +- faaPath = '%s/faa' % workingDir ++ fastaPath = '%s/fastaSP' % workingDir ++ faaPath = '%s/faaSP' % workingDir + step13(step11Output, fastaFile1, fastaFile2, hmmFolder, step13OutputFile1, fastaPath, faaPath, step13OutputFile2) + step14Output = step13OutputFile1 + '.remove' + step14(step13OutputFile1, step14Output) +@@ -844,7 +848,7 @@ + def control(fastaFile1, fastaFile2, hmmFile, seedFile, threshold, outputFile): + baseFile = os.path.basename(fastaFile1) + fastaName = baseFile.replace('.1.fasta','') +- baseDir = os.path.dirname(fastaFile1) ++ baseDir = abspath(os.path.dirname(fastaFile1)) + patternDir = '%s/Protein' % baseDir + + if not os.path.isdir(patternDir): diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb new file mode 100644 index 00000000000..8fd96339019 --- /dev/null +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'CmdCp' + +name = 'Short-Pair' +version = '20170125' + +homepage = 'https://sourceforge.net/projects/short-pair' +description = "Sensitive Short Read Homology Search for Paired-End Reads" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [{'download_filename': 'Short-Pair.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3'] + +patches = ['Short-Pair-20170125-Python3fix.patch'] + +dependencies = [ + ('Python', '3.9.6'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2021.10') +] + +exts_list = [ + ('numpy', '1.22.0', { + 'source_urls': ['https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/'], + 'sources': ['%(name)s-%(version)s.zip'], + }) +] + +cmds_map = [('.*', "$CXX $CXXFLAGS -w -o DNA2Protein DNA2Protein.cpp")] + +files_to_copy = [(['DNA2Protein', 'get_hmm.sh', 'hmmer3_pipeline_missing_end.sh', 'Short-Pair.py'], 'bin')] + +fix_python_shebang_for = ['bin/Short-Pair.py'] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/*"] + +exts_defaultclass = 'PythonBundle' + +sanity_check_paths = { + 'files': ['bin/DNA2Protein', 'bin/get_hmm.sh', 'bin/hmmer3_pipeline_missing_end.sh', 'bin/Short-Pair.py'], + 'dirs': [], +} + +sanity_check_commands = ["python3 bin/Short-Pair.py -h"] + +moduleclass = 'bio' From 0a5adc1be5211013e9cf103d613e464491a31ba7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 13 Jan 2022 20:53:27 +0100 Subject: [PATCH 450/528] adding easyconfigs: SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb, hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb, pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb and patches: numpy-1.16.6_add_flexiblas_detection.patch, numpy-1.16.6_handle_failing_linalg_test.patch --- ...sis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb | 25 +++ ...nd11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb | 25 +++ ...bundle-2021.10-foss-2021b-Python-2.7.18.eb | 84 ++++++++ ...numpy-1.16.6_add_flexiblas_detection.patch | 181 ++++++++++++++++++ ...py-1.16.6_handle_failing_linalg_test.patch | 17 ++ 5 files changed, 332 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..1a30b129637 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '4.57.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3c4369a4b0a1348561048bcda5f1db951a1b8e2a514ea8e8c70d36e656bf6fa0'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '2.7.18')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..f393fb93837 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,25 @@ +name = 'pybind11' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['616d1c42e4cf14fa27b2a4ff759d7d7b33006fdc5ad8fd603bb2c22622f27020'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Eigen', '3.3.9'), +] + +dependencies = [('Python', '2.7.18')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..f806bd48d7a --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '4.57.1', versionsuffix), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('pybind11', '2.7.1', versionsuffix), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.16.6', { + 'patches': [ + 'numpy-1.16.2_relax-long-complex-test.patch', + 'numpy-1.16.6_add_flexiblas_detection.patch', + 'numpy-1.16.6_handle_failing_linalg_test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip + # numpy-1.16.2_relax-long-complex-test.patch + '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', + # numpy-1.16.6_add_flexiblas_detection.patch + '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5', + # numpy-1.16.6_handle_failing_linalg_test.patch + 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.2', { + 'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('scipy', '1.2.3', { + 'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'], + 'prebuildopts': 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ', + 'checksums': [ + 'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57', # scipy-1.2.3.tar.gz + # scipy-1.2.3_fix_nan_problem_in_vi.patch + '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d', + ], + }), + ('mpi4py', '3.1.1', { + 'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '0.24.2', { + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch new file mode 100644 index 00000000000..02528b44bc3 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch @@ -0,0 +1,181 @@ +Add flexiblas detection to numpy. +This is just a copy of the openblas detection with name changed. + +Åke Sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/distutils/system_info.py numpy-1.16.6/numpy/distutils/system_info.py +--- numpy-1.16.6.orig/numpy/distutils/system_info.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/distutils/system_info.py 2022-01-13 16:48:14.754235308 +0100 +@@ -20,6 +20,7 @@ + blas_info + lapack_info + openblas_info ++ flexiblas_info + blis_info + blas_opt_info # usage recommended + lapack_opt_info # usage recommended +@@ -395,6 +396,9 @@ + # openblas with embedded lapack + 'openblas_lapack': openblas_lapack_info, # use blas_opt instead + 'openblas_clapack': openblas_clapack_info, # use blas_opt instead ++ 'flexiblas': flexiblas_info, # use blas_opt instead ++ 'flexiblas_lapack': flexiblas_lapack_info, # use blas_opt instead ++ 'flexiblas_clapack': flexiblas_clapack_info, # use blas_opt instead + 'blis': blis_info, # use blas_opt instead + 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead + 'blas_mkl': blas_mkl_info, # use blas_opt instead +@@ -1549,6 +1553,16 @@ + self.set_info(**lapack_mkl_info) + return + ++ flexiblas_info = get_info('flexiblas_lapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ ++ flexiblas_info = get_info('flexiblas_clapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas_lapack') + if openblas_info: + self.set_info(**openblas_info) +@@ -1633,6 +1647,11 @@ + self.set_info(**blis_info) + return + ++ flexiblas_info = get_info('flexiblas') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas') + if openblas_info: + self.set_info(**openblas_info) +@@ -1749,6 +1768,126 @@ + return res + + ++class flexiblas_info(blas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ return True ++ ++ def calc_info(self): ++ c = customized_ccompiler() ++ ++ lib_dirs = self.get_lib_dirs() ++ ++ flexiblas_libs = self.get_libs('libraries', self._lib_names) ++ if flexiblas_libs == self._lib_names: # backward compat with 1.8.0 ++ flexiblas_libs = self.get_libs('flexiblas_libs', self._lib_names) ++ ++ info = self.check_libs(lib_dirs, flexiblas_libs, []) ++ ++ if c.compiler_type == "msvc" and info is None: ++ from numpy.distutils.fcompiler import new_fcompiler ++ f = new_fcompiler(c_compiler=c) ++ if f and f.compiler_type == 'gnu95': ++ # Try gfortran-compatible library files ++ info = self.check_msvc_gfortran_libs(lib_dirs, flexiblas_libs) ++ # Skip lapack check, we'd need build_ext to do it ++ assume_lapack = True ++ elif info: ++ assume_lapack = False ++ info['language'] = 'c' ++ ++ if info is None: ++ return ++ ++ # Add extra info for OpenBLAS ++ extra_info = self.calc_extra_info() ++ dict_append(info, **extra_info) ++ ++ if not (assume_lapack or self.check_embedded_lapack(info)): ++ return ++ ++ info['define_macros'] = [('HAVE_CBLAS', None)] ++ self.set_info(**info) ++ ++ def check_msvc_gfortran_libs(self, library_dirs, libraries): ++ # First, find the full path to each library directory ++ library_paths = [] ++ for library in libraries: ++ for library_dir in library_dirs: ++ # MinGW static ext will be .a ++ fullpath = os.path.join(library_dir, library + '.a') ++ if os.path.isfile(fullpath): ++ library_paths.append(fullpath) ++ break ++ else: ++ return None ++ ++ # Generate numpy.distutils virtual static library file ++ tmpdir = os.path.join(os.getcwd(), 'build', 'flexiblas') ++ if not os.path.isdir(tmpdir): ++ os.makedirs(tmpdir) ++ ++ info = {'library_dirs': [tmpdir], ++ 'libraries': ['flexiblas'], ++ 'language': 'f77'} ++ ++ fake_lib_file = os.path.join(tmpdir, 'flexiblas.fobjects') ++ fake_clib_file = os.path.join(tmpdir, 'flexiblas.cobjects') ++ with open(fake_lib_file, 'w') as f: ++ f.write("\n".join(library_paths)) ++ with open(fake_clib_file, 'w') as f: ++ pass ++ ++ return info ++ ++class flexiblas_lapack_info(flexiblas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ res = False ++ c = customized_ccompiler() ++ ++ tmpdir = tempfile.mkdtemp() ++ s = """void zungqr_(); ++ int main(int argc, const char *argv[]) ++ { ++ zungqr_(); ++ return 0; ++ }""" ++ src = os.path.join(tmpdir, 'source.c') ++ out = os.path.join(tmpdir, 'a.out') ++ # Add the additional "extra" arguments ++ try: ++ extra_args = info['extra_link_args'] ++ except Exception: ++ extra_args = [] ++ if sys.version_info < (3, 5) and sys.version_info > (3, 0) and c.compiler_type == "msvc": ++ extra_args.append("/MANIFEST") ++ try: ++ with open(src, 'wt') as f: ++ f.write(s) ++ obj = c.compile([src], output_dir=tmpdir) ++ try: ++ c.link_executable(obj, out, libraries=info['libraries'], ++ library_dirs=info['library_dirs'], ++ extra_postargs=extra_args) ++ res = True ++ except distutils.ccompiler.LinkError: ++ res = False ++ finally: ++ shutil.rmtree(tmpdir) ++ return res ++ ++class flexiblas_clapack_info(flexiblas_lapack_info): ++ _lib_names = ['flexiblas', 'lapack'] ++ + class openblas_info(blas_info): + section = 'openblas' + dir_env_var = 'OPENBLAS' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch new file mode 100644 index 00000000000..d85fb475809 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch @@ -0,0 +1,17 @@ +linalg/test_nan is marked xfail in at least 1.21.3 +Do so here too since it fails with newer openblas/compiler versions. + +Åke sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py numpy-1.16.6/numpy/linalg/tests/test_linalg.py +--- numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/linalg/tests/test_linalg.py 2022-01-13 17:21:36.658857878 +0100 +@@ -740,6 +740,9 @@ + for A, p in itertools.product(As, p_neg): + linalg.cond(A, p) + ++ @pytest.mark.xfail(True, run=False, ++ reason="Platform/LAPACK-dependent failure, " ++ "see gh-18914") + def test_nan(self): + # nans should be passed through, not converted to infs + ps = [None, 1, -1, 2, -2, 'fro'] From da9ed4e7ab064bcdd9c97d203073141e8c6bd29a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 21:38:09 +0100 Subject: [PATCH 451/528] adding easyconfigs: texlive-20210324-GCC-11.2.0.eb --- .../graphite2-1.3.14-GCCcore-11.2.0.eb | 27 ++++++++ .../p/poppler/poppler-22.01.0-GCC-11.2.0.eb | 59 +++++++++++++++++ .../t/texlive/texlive-20210324-GCC-11.2.0.eb | 63 +++++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f60b4dd57e1 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..ad8abb534ac --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '22.01.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.9.6', '-bare'), +] + +dependencies = [ + ('freetype', '2.11.0'), + ('fontconfig', '2.13.94'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('NSS', '3.69'), + ('LibTIFF', '4.3.0'), + ('Qt5', '5.15.2'), + ('Boost', '1.77.0'), + ('cairo', '1.16.0'), + ('OpenJPEG', '2.4.0'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['7d3493056b5b86413e5c693c2cae02c5c06cd8e618d14c2c31e2c84b67b2313e'], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.11', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2cec05cd1bb03af98a8b06a1e22f6e6e1a65b1e2f3816cb3069bb0874825f08c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb new file mode 100644 index 00000000000..b00d0026d53 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20210324' + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/2021/', + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz', + } +] +checksums = ['74eac0855e1e40c8db4f28b24ef354bd7263c1f76031bdc02b52156b572b7a1d'] + +dependencies = [ + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('libGLU', '9.0.2'), + ('Perl', '5.34.0'), + ('HarfBuzz', '2.8.2'), + ('poppler', '22.01.0'), + ('cairo', '1.16.0'), + ('fontconfig', '2.13.94'), + ('zlib', '1.2.11'), + ('graphite2', '1.3.14'), +] + +postinstallcmds = [ + 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' + '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' +] + +modextrapaths = { + 'PATH': 'bin/%(arch)s-linux', + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', +} +modextravars = { + 'TEXMFHOME': '%(installdir)s/texmf-dist' +} + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +moduleclass = 'devel' From 497c50f8b1fbb2820473285a502be091bd035b19 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 10:45:51 +0100 Subject: [PATCH 452/528] Adjust versxion of backports.entry_points_selectable make Python-2.7.18-GCCcore-11.2.0.eb match Python-3.9.6-GCCcore-11.2.0.eb --- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index 72ceefe329f..c9a13925842 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -173,8 +173,8 @@ exts_list = [ ('platformdirs', '2.0.2', { 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], }), - ('backports.entry_points_selectable', '1.1.1', { - 'checksums': ['914b21a479fde881635f7af5adc7f6e38d6b274be32269070c53b698c60d5386'], + ('backports.entry_points_selectable', '1.1.0', { + 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], }), ('virtualenv', '20.7.0', { 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], From 57b9c9bc59dfb56bd0105bcdfab9cbd27c5d06b7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 12:10:40 +0100 Subject: [PATCH 453/528] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index f2c7ad44957..fd1240cbc56 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -32,9 +32,9 @@ separate_build_dir = True buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" -install_cmd = """mkdir -p %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" +install_cmd = "mkdir -p %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" sanity_check_paths = { From 158751b1304dd4a58bd994edb473a2fd102ffb1a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 12:45:19 +0100 Subject: [PATCH 454/528] adding easyconfigs: IPython-5.10.0-foss-2021b-Python-2.7.18.eb, matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb, Tkinter-2.7.18-GCCcore-11.2.0.eb --- ...IPython-5.10.0-foss-2021b-Python-2.7.18.eb | 152 ++++++++++++++++++ ...tplotlib-2.2.5-foss-2021b-Python-2.7.18.eb | 60 +++++++ .../Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb | 24 +++ 3 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..aedca6f38f9 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,152 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '2.7.18'), + ('ZeroMQ', '4.3.4'), + ('matplotlib', '2.2.5', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['d1f9e2d02bb0900ddef7b6af114aca3a5cf3dc43b9de1f19d37c4aedbc724fee'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '1.0.15', { + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('traitlets', '4.3.3', { + 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], + }), + ('parso', '0.7.1', { + 'checksums': ['caba44724b994a8a5e086460bb212abc5a8bc46951bf4a9a1210745953622eb9'], + }), + ('jedi', '0.17.2', { + 'checksums': ['86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('nbconvert', '5.6.1', { + 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], + }), + ('nbformat', '4.4.0', { + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter-packaging', '0.4.0', { + 'checksums': ['d89134d2df88c30098bce0f8d8fb07b988ef0f616775dbd4b82dac9562b5cae6'], + }), + ('jupyterlab_widgets', '0.6.15', { + 'checksums': ['2954919a6a04a48230b904e60f00d839e339f15ee9748d4172c8ae403ad4fb47'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '3.3.1', { + 'checksums': ['306483a5a9795474160ad57fce3ddd1b50551e981eed8e15a582d34cef28aafa'], + }), + ('vcversioner', '2.16.0.0', { + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('pandocfilters', '1.4.3', { + 'checksums': ['bc63fbb50534b4b1f8ebe1860889289e8af94a23bff7445259592df25a3906eb'], + }), + ('pyzmq', '19.0.2', { + 'modulename': 'zmq', + 'checksums': ['296540a065c8c21b26d63e3cea2d1d57902373b16e4256afe46422691903a438'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('terminado', '0.8.3', { + 'use_pip': False, + 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], + }), + ('backports_abc', '0.5', { + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('tornado', '5.1.1', { + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('jupyter_client', '5.3.5', { + 'checksums': ['5efdf4131124d4a0d5789101e74827022585f172d2f4b60cf6fa98e0a7511b25'], + }), + ('ipykernel', '4.10.1', { + 'checksums': ['eeb74b2bcfe0ced5a7900361f98fa1171288aa47ed4b522efe5acb167c6cf5fb'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('notebook', '5.7.13', { + 'checksums': ['b64adb32eafa775b299227e92948c7fa4ec837624dc6243b90fef90f15b7a0bd'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..57137691145 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.1.0', { + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], + }), +] + +postinstallcmds = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..09c8f6a9b3e --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'Tkinter' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.11'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' From 68378e863b1a2ae2688dcbd5acfb04d23b0a607b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 14 Jan 2022 11:47:25 +0000 Subject: [PATCH 455/528] adding easyconfigs: TALYS-1.95-GCCcore-9.3.0.eb, TALYS-1.95-GCCcore-10.3.0.eb --- .../t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb | 41 +++++++++++++++++++ .../t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3cb0dd44e83 --- /dev/null +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CmdCp' + +name = 'TALYS' +version = '1.95' + +homepage = 'https://tendl.web.psi.ch/tendl_2019/talys.html' +description = "TALYS is a nuclear reaction program." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'noopt': True} + +source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] +sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] + +builddependencies = [('binutils', '2.36.1')] + +start_dir = 'source' + +# Use environment variable to set structure directory path +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed += ' -e "s|character*132 path|character*256 path|g" ' +local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' +# Also strip hardcoded talys path in verify script +local_sed += 'sed -i "/talys=.*/d" ../samples/verify ' + +cmds_map = [('.*', '%s && $FC $FFLAGS $FCFLAGS -o talys *.f' % local_sed)] + +files_to_copy = [(['%(namelower)s'], 'bin'), 'structure', 'samples'] + +sanity_check_paths = { + 'files': ['bin/talys'], + 'dirs': ['bin', 'samples', 'structure'], +} + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s/samples && ./verify"] + +modextravars = {'TALYS_STRUCTURE_DIR': '%(installdir)s/structure'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d5f52ba4a59 --- /dev/null +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CmdCp' + +name = 'TALYS' +version = '1.95' + +homepage = 'https://tendl.web.psi.ch/tendl_2019/talys.html' +description = "TALYS is a nuclear reaction program." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'noopt': True} + +source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] +sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] + +builddependencies = [('binutils', '2.34')] + +start_dir = 'source' + +# Use environment variable to set structure directory path +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed += ' -e "s|character*132 path|character*256 path|g" ' +local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' +# Also strip hardcoded talys path in verify script +local_sed += 'sed -i "/talys=.*/d" ../samples/verify ' + +cmds_map = [('.*', '%s && $FC $FFLAGS $FCFLAGS -o talys *.f' % local_sed)] + +files_to_copy = [(['%(namelower)s'], 'bin'), 'structure', 'samples'] + +sanity_check_paths = { + 'files': ['bin/talys'], + 'dirs': ['samples', 'structure'], +} + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s/samples && ./verify"] + +modextravars = {'TALYS_STRUCTURE_DIR': '%(installdir)s/structure'} + +moduleclass = 'phys' From 1cdb78bb20fc732666a9c8aa8cdba00f9ea22ed3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 14 Jan 2022 12:31:08 +0000 Subject: [PATCH 456/528] Linting --- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb index 3cb0dd44e83..0a6c88f179b 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.36.1')] start_dir = 'source' # Use environment variable to set structure directory path -local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' local_sed += ' -e "s|character*132 path|character*256 path|g" ' local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' # Also strip hardcoded talys path in verify script diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb index d5f52ba4a59..28297ff22e5 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.34')] start_dir = 'source' # Use environment variable to set structure directory path -local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' local_sed += ' -e "s|character*132 path|character*256 path|g" ' local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' # Also strip hardcoded talys path in verify script From 5b11a7971aca95a1cc0ef017aa7a6e41d332e8c6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 14:14:04 +0100 Subject: [PATCH 457/528] Add missing deps and turn on sanity_pip_check --- .../IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb index aedca6f38f9..d58979770fb 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb @@ -73,6 +73,12 @@ exts_list = [ ('jupyter-packaging', '0.4.0', { 'checksums': ['d89134d2df88c30098bce0f8d8fb07b988ef0f616775dbd4b82dac9562b5cae6'], }), + ('jupyterlab_launcher', '0.11.2', { + 'checksums': ['236a647f4c3f8417413643a918a893a5f662fb5d2fdccce2fd101e3cca2e7fd1'], + }), + ('jupyterlab', '0.33.12', { + 'checksums': ['04a14b38b218c87731b519ff0f7e133b28a613ad944617ac7e07480d6a36eb5f'], + }), ('jupyterlab_widgets', '0.6.15', { 'checksums': ['2954919a6a04a48230b904e60f00d839e339f15ee9748d4172c8ae403ad4fb47'], }), @@ -139,6 +145,8 @@ exts_list = [ }), ] +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], @@ -149,4 +157,6 @@ sanity_check_commands = [ "jupyter notebook --help", ] +sanity_pip_check = True + moduleclass = 'tools' From 76a1d28606129243211b977adeadaec49be75f1a Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 14 Jan 2022 14:46:33 +0100 Subject: [PATCH 458/528] adding easyconfigs: PAML-4.9j-GCCcore-11.2.0.eb --- .../p/PAML/PAML-4.9j-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5b009111831 --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +builddependencies = [('binutils', '2.37')] + +start_dir = 'src' + +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['baseml.ctl', 'codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + +moduleclass = 'bio' From 8532ea852d898b779f35273a10bc3af8e8c5ab10 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 14 Jan 2022 15:17:17 +0100 Subject: [PATCH 459/528] Removed typo --- easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 154cc13b16c..20f3e803269 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -12,7 +12,7 @@ description = """MinPath (Minimal set of Pathways) is a parsimony approach for b toolchain = {'name': 'intel', 'version': '2021b'} -source_urls = ['https://github.com/mgtools/MinPath/archive/'], +source_urls = ['https://github.com/mgtools/MinPath/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] checksums = [ From c6b25a856d7a4031583374f8f8e0d69d0e119932 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 15:51:49 +0100 Subject: [PATCH 460/528] DualSPHysics: Fixes sanity check and updates patch header --- ...SPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 25 ++++++++----------- .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 23 +++++++---------- .../d/DualSPHysics/DualSPHysics-5.0.175.patch | 2 ++ 3 files changed, 21 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 33a9ac4cc9f..46e679af552 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -24,7 +24,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s.patch'] checksums = [ 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', # v5.0.175.tar.gz - '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', # DualSPHysics-5.0.175.patch + 'b2fad86d99e31fe2e1b5c65bab60a4f14362401b6de00a395b3a1bd13f608366', # DualSPHysics-5.0.175.patch ] srcdir = 'src/source' @@ -42,22 +42,17 @@ install_cmd = "mkdir -p %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" +local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord', + 'DualSPHysics4.0_LiquidGas', 'DualSPHysics4.0_LiquidGasCPU', 'DualSPHysics5.0', + 'DualSPHysics5.0CPU', 'DualSPHysics5.0_NNewtonian', 'DualSPHysics5.0_NNewtonianCPU'] + sanity_check_paths = { - 'files': [ - 'bin/GenCase_linux64', - 'bin/PartVTK_linux64', - 'bin/IsoSurface_linux64', - 'bin/MeasureTool_linux64', - 'bin/GenCase_MkWord_linux64', - 'bin/DualSPHysics4.0_LiquidGas_linux64', - 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', - 'bin/DualSPHysics5.0_linux64', - 'bin/DualSPHysics5.0CPU_linux64', - 'bin/DualSPHysics5.0_NNewtonian_linux64', - 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', - ], - 'dirs': ["lib"], + 'files': ['bin/%s_linux64' % x for x in local_bins], + 'dirs': ["lib", "bin"], } +sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] + + moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index fd1240cbc56..347fbb54bb2 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -36,22 +36,17 @@ install_cmd = "mkdir -p %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" +local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord', + 'DualSPHysics4.0_LiquidGas', 'DualSPHysics4.0_LiquidGasCPU', 'DualSPHysics5.0', + 'DualSPHysics5.0CPU', 'DualSPHysics5.0_NNewtonian', 'DualSPHysics5.0_NNewtonianCPU'] + sanity_check_paths = { - 'files': [ - 'bin/GenCase_linux64', - 'bin/PartVTK_linux64', - 'bin/IsoSurface_linux64', - 'bin/MeasureTool_linux64', - 'bin/GenCase_MkWord_linux64', - 'bin/DualSPHysics4.0_LiquidGas_linux64', - 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', - 'bin/DualSPHysics5.0_linux64', - 'bin/DualSPHysics5.0CPU_linux64', - 'bin/DualSPHysics5.0_NNewtonian_linux64', - 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', - ], - 'dirs': ["lib"], + 'files': ['bin/%s_linux64' % x for x in local_bins], + 'dirs': ["lib", "bin"], } +sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] + + moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch index 556373c9719..adad3dd6d3e 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch @@ -1,3 +1,5 @@ +Author: Robert Mijakovic +Adds newly supported code generation for CUDA 11. diff -Naur DualSPHysics-5.0.175/src/source/CMakeLists.txt DualSPHysics-5.0.175/src/source/CMakeLists.txt --- DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-02-25 18:46:13.000000000 +0100 +++ DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-10-13 18:46:17.000000000 +0200 From 7471b0bf7438d7274ee74ccc82c54cf262fcda37 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 14 Jan 2022 16:03:49 +0100 Subject: [PATCH 461/528] adding easyconfigs: PREQUAL-1.02-GCCcore-11.2.0.eb --- .../p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..971db7cb571 --- /dev/null +++ b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'PREQUAL' +version = '1.02' + +homepage = 'https://github.com/simonwhelan/prequal' +description = 'A program to identify and mask regions with non-homologous adjacent characters in FASTA files.' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [{ + 'filename': '%(namelower)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/simonwhelan', + 'repo_name': '%(namelower)s', + 'commit': '67da42cf4761ed5fd8298eb4432ca8f54c487398', + }, +}] +checksums = ['28ae8ab4825afca103db8c90d79f77699186f90fdb3c059875975e880e70be1e'] + +builddependencies = [ + ('binutils', '2.37'), +] + +files_to_copy = ['prequal', 'LICENSE'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['prequal'], + 'dirs': [], +} + +moduleclass = 'bio' From 47a94c712748005dd68f65fa681da609bcfa9870 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 14 Jan 2022 17:18:49 +0100 Subject: [PATCH 462/528] fix chesum of elbencho v2.0-3 sources --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 905272ac462..2b4169ce7ff 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ github_account = 'breuner' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] +checksums = ['24dc396855d60192252417bd962cf67c4787baba04345c81ff71fe9981777238'] files_to_copy = ["bin"] sanity_check_paths = { From 3b40762d0529566bc576578a455f814dbf0395da Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 14 Jan 2022 17:26:57 +0100 Subject: [PATCH 463/528] fix codestyle and add sanity_check_commands to elbencho v2.0-3 --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 2b4169ce7ff..1ff05206f4b 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -6,7 +6,6 @@ version = "2.0-3" homepage = "https://github.com/breuner/elbencho" description = """ A distributed storage benchmark for files, objects & blocks with support for GPUs""" - toolchain = {'name': 'GCC', 'version': '10.3.0'} dependencies = [ @@ -21,12 +20,15 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['24dc396855d60192252417bd962cf67c4787baba04345c81ff71fe9981777238'] -files_to_copy = ["bin"] +buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' + +files_to_copy = ['bin'] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in - ['elbencho', 'elbencho-unstripped']], + 'files': 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], 'dirs': [], } -buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' +sanity_check_commands = [('elbencho', '--help')] + moduleclass = 'tools' From 26ba0434ee6fe4b1d0360ed7cecaa7a56f6ba9ba Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 14 Jan 2022 18:36:03 +0200 Subject: [PATCH 464/528] Add missing dependecy easyconfig for tn93 --- .../t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e74ef4838b1 --- /dev/null +++ b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'tn93' +version = '1.0.7' + +homepage = 'https://github.com/veg/tn93' +description = """his is a simple program meant to compute pairwise distances between + aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] + +unpack_options = '--strip-components=1' + +separate_build_dir = True + +buildininstalldir = True + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + + +build_cmd = ' make ' + + +# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file +# will allways end up with /usr/local as the install prefix +install_cmd = 'mkdir -p %(installdir)s/bin &&' +install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' +install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' +install_cmd += ' %(installdir)s/bin ' + +sanity_check_paths = { + 'files': ['bin/tn93'], + 'dirs': [], +} + +moduleclass = 'bio' From 42d8e25b170a3232a51b7eb8c7a9c261cdea1384 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 14 Jan 2022 18:37:51 +0200 Subject: [PATCH 465/528] Add requested changes: remove pypi urls and add sanity_check_commands --- .../h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index 9137968d933..dc23ffb4a39 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -28,32 +28,25 @@ sanity_pip_check = True exts_list = [ ('hyphy-python', '0.1.10', { 'modulename': 'HyPhy', - 'source_urls': ['https://pypi.python.org/packages/source/h/hyphy-python'], 'checksums': ['b83f7e890c0c21b301c1c761967bd6328df9fad972653888b02baad71055c186'], }), ('fakemp', '0.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/fakemp'], 'checksums': ['320885d5851e0c568cd4247fa81e48f055e435822643e5bda9d82edc53c3b938'], }), ('hppy', '0.9.9', { - 'source_urls': ['https://pypi.python.org/packages/source/h/hppy'], 'checksums': ['9112acc888c51c14a88669f084a7ebf39fa62bdd47924a1e3cee6824cfbc4610'], }), ('tornado', '6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], }), ('bioext', '0.19.9', { 'modulename': 'BioExt', - 'source_urls': ['https://pypi.python.org/packages/source/b/bioext'], 'checksums': ['bada8d7e83928a8c934e1e482bc945f43a3234c6c4ea3afcef7fa34c0ea610a3'], }), ('hivclustering', '1.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/h/hivclustering'], 'checksums': ['673fa81b6b44ae7a7bfa32897bc01c26cfe807052aadc3d1f5a729b0df3a335f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hivtrace'], 'checksums': ['f4aabd2bbc326aecb9ab22de8f6877628f908cfa8eee458feb06d48bb19425e6'], }), ] @@ -69,4 +62,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'hivtrace --help', +] + moduleclass = 'bio' From a1399fd3401dddfa8bc251ba11200e6902a2846d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 14 Jan 2022 17:39:26 +0100 Subject: [PATCH 466/528] adding easyconfigs: canu-2.2-GCCcore-11.2.0.eb --- .../c/canu/canu-2.2-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..946fb4dd038 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.2' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.37'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.33.1', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.34.0'), + ('gnuplot', '5.4.2'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogart', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From 42a6b580b89a393afafa8560ca7611603753900e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 17:58:27 +0100 Subject: [PATCH 467/528] DualSPHysics: Removes bin from sanity_check_path --- .../DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 46e679af552..45622c59260 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -49,7 +49,7 @@ local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord sanity_check_paths = { 'files': ['bin/%s_linux64' % x for x in local_bins], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index 347fbb54bb2..8f34229debc 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -43,7 +43,7 @@ local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord sanity_check_paths = { 'files': ['bin/%s_linux64' % x for x in local_bins], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] From 737b2c92f8f339e94973abb0e4320282626cd2b7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Jan 2022 18:14:46 +0100 Subject: [PATCH 468/528] dont use git_config; add sanity_check_commands --- .../p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb index 971db7cb571..f1e9f015992 100644 --- a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb @@ -2,21 +2,20 @@ easyblock = 'MakeCp' name = 'PREQUAL' version = '1.02' +local_commit = '67da42c' homepage = 'https://github.com/simonwhelan/prequal' description = 'A program to identify and mask regions with non-homologous adjacent characters in FASTA files.' toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +github_account = 'simonwhelan' +source_urls = [GITHUB_SOURCE] sources = [{ - 'filename': '%(namelower)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/simonwhelan', - 'repo_name': '%(namelower)s', - 'commit': '67da42cf4761ed5fd8298eb4432ca8f54c487398', - }, + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, }] -checksums = ['28ae8ab4825afca103db8c90d79f77699186f90fdb3c059875975e880e70be1e'] +checksums = ['f0663f6b324dbc6088450f32b3087a2b6ea07138e25850987608b9bb23007d1a'] builddependencies = [ ('binutils', '2.37'), @@ -31,4 +30,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['prequal -h | grep "^Usage:"'] + moduleclass = 'bio' From 1a2754ae694bd6701ff46a26c34207aceb59d778 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Jan 2022 20:02:13 +0100 Subject: [PATCH 469/528] adding easyconfigs: mapDamage-2.2.1-foss-2021b.eb, seqtk-1.3-GCC-11.2.0.eb --- .../m/mapDamage/mapDamage-2.2.1-foss-2021b.eb | 30 +++++++++++++++++ .../s/seqtk/seqtk-1.3-GCC-11.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb new file mode 100644 index 00000000000..1f99a9c4a15 --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] + +dependencies = [ + ('Python', '3.9.6'), + ('seqtk', '1.3'), + ('Pysam', '0.17.0'), + ('R', '4.1.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..75d5727fb85 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"] + +moduleclass = 'bio' From aa44433dacf0e565e249cdc26cb0cfc29a39869f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Jan 2022 20:21:30 +0100 Subject: [PATCH 470/528] Fix OpenMPI memleak that heavily affects CP2K, SIESTA, QUantumESPRESSO, VASP --- ...MPI-4.0.5-6-pml-ucx-datatype-memleak.patch | 66 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb | 3 + .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 3 + .../OpenMPI-4.0.5-iccifort-2020.4.304.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb | 7 +- ...MPI-4.1.0-1-pml-ucx-datatype-memleak.patch | 58 ++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 3 + .../OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 3 + 12 files changed, 157 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch new file mode 100644 index 00000000000..1e5111c47e5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch @@ -0,0 +1,66 @@ +From f5c391288b766a96cb5c5d0b7164e9cf8795921f Mon Sep 17 00:00:00 2001 +From: Sergey Oblomov +Date: Thu, 15 Jul 2021 19:24:40 +0300 +Subject: [PATCH] PML/UCX/DATATYPE: fixed memory leak + +- fixed memory leak in datatype processin + +Signed-off-by: Sergey Oblomov +(cherry picked from commit 4145b9f) +--- + ompi/mca/pml/ucx/pml_ucx_datatype.c | 28 +++++++++++++++++----------- + 1 file changed, 17 insertions(+), 11 deletions(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.c b/ompi/mca/pml/ucx/pml_ucx_datatype.c +index 5b1b8ccbed3..7277aef64bc 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.c ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.c +@@ -212,14 +212,23 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_datatype_type_size(datatype, &size); + PML_UCX_ASSERT(size > 0); + ucp_datatype = ucp_dt_make_contig(size); +- goto out; +- } +- +- status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); +- if (status != UCS_OK) { +- PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); +- ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ PML_UCX_VERBOSE(7, "created contig UCX datatype 0x%"PRIx64, ++ ucp_datatype) ++ } else { ++ status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, ++ datatype, &ucp_datatype); ++ if (status != UCS_OK) { ++ int err = MPI_ERR_INTERN; ++ PML_UCX_ERROR("Failed to create UCX datatype for %s", ++ datatype->name); ++ /* TODO: this error should return to the caller and invoke an error ++ * handler from the MPI API call. ++ * For now, it is fatal. */ ++ ompi_mpi_errors_are_fatal_comm_handler(NULL, &err, ++ "Failed to allocate " ++ "datatype structure"); ++ } ++ PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + } + + /* Add custom attribute, to clean up UCX resources when OMPI datatype is +@@ -238,8 +247,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + } +-out: +- PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + + #ifdef HAVE_UCP_REQUEST_PARAM_T + UCS_STATIC_ASSERT(sizeof(datatype->pml_data) >= sizeof(pml_ucx_datatype_t*)); +@@ -249,7 +256,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + #else + datatype->pml_data = ucp_datatype; + #endif +- + return ucp_datatype; + } + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 110d6438af5..1536146190d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index 63cf6be8173..c399450ab49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 503f955baf2..383370dd6f5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -13,12 +13,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 12093c5a847..3746daadf8e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index d33ec82375b..de0f5b3d2e1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb index 98875b6d1cf..cfb51234ef4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', +] checksums = [ '8f2d159d2d846979b1380e9552f56e4365f5ec71d54a05077ddb244719d70fc3', # openmpi-4.0.6.tar.gz # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch new file mode 100644 index 00000000000..29266832b1b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch @@ -0,0 +1,58 @@ +From 080e54b07d5976407daf8c607a5d2b80ee40684d Mon Sep 17 00:00:00 2001 +From: Sergey Oblomov +Date: Mon, 19 Apr 2021 16:50:46 +0300 +Subject: [PATCH] PML/UCX/DATATYPE: fixed memory leak + +- fixed memory leak in datatype processing + +Signed-off-by: Sergey Oblomov +(cherry picked from commit 4145b9f00b9a9c2e5326044b765ee3d1b743ccbf) +--- + ompi/mca/pml/ucx/pml_ucx_datatype.c | 27 +++++++++++++++++---------- + 1 file changed, 17 insertions(+), 10 deletions(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.c b/ompi/mca/pml/ucx/pml_ucx_datatype.c +index 5b1b8ccbed3..8b55e773e7a 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.c ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.c +@@ -212,14 +212,23 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_datatype_type_size(datatype, &size); + PML_UCX_ASSERT(size > 0); + ucp_datatype = ucp_dt_make_contig(size); +- goto out; +- } +- +- status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); +- if (status != UCS_OK) { +- PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); +- ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ PML_UCX_VERBOSE(7, "created contig UCX datatype 0x%"PRIx64, ++ ucp_datatype) ++ } else { ++ status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, ++ datatype, &ucp_datatype); ++ if (status != UCS_OK) { ++ int err = MPI_ERR_INTERN; ++ PML_UCX_ERROR("Failed to create UCX datatype for %s", ++ datatype->name); ++ /* TODO: this error should return to the caller and invoke an error ++ * handler from the MPI API call. ++ * For now, it is fatal. */ ++ ompi_mpi_errors_are_fatal_comm_handler(NULL, &err, ++ "Failed to allocate " ++ "datatype structure"); ++ } ++ PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + } + + /* Add custom attribute, to clean up UCX resources when OMPI datatype is +@@ -238,8 +247,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + } +-out: +- PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + + #ifdef HAVE_UCP_REQUEST_PARAM_T + UCS_STATIC_ASSERT(sizeof(datatype->pml_data) >= sizeof(pml_ucx_datatype_t*)); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index 084adbc63ff..b82c542c424 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz @@ -20,6 +21,8 @@ checksums = [ # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 2728bb55635..2953c5af9f4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -21,6 +22,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index d1e63535d53..593e8e3be27 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -13,6 +13,7 @@ patches = [ 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', 'OpenMPI-4.1.1_pmix3x-protection.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -22,6 +23,8 @@ checksums = [ '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 6d64daf9054..05a6b8d93de 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -21,6 +22,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ From cfb07b7a45dd9e747629f47956f03632dfc5bd2f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Jan 2022 20:51:51 +0100 Subject: [PATCH 471/528] and missing trailing comma (,) --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 2 +- .../o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 2953c5af9f4..57c38134baa 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 05a6b8d93de..523bf0bb069 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ From 3d73b6266a3b5914573451b732e3a565f71591a4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Jan 2022 01:24:28 +0100 Subject: [PATCH 472/528] fix sanity checks of elbencho v2.0-3 --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 1ff05206f4b..2465c26d165 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -25,7 +25,7 @@ buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS" files_to_copy = ['bin'] sanity_check_paths = { - 'files': 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], + 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], 'dirs': [], } From 7235f3c4cdb0671e96782918db743cb35fc9e72d Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 15 Jan 2022 13:13:21 +0200 Subject: [PATCH 473/528] Add requested changes to the easyconfig --- .../t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4f9cb55bea9 --- /dev/null +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'TN93' +version = '1.0.7' + +homepage = 'https://github.com/veg/tn93' +description = """This is a simple program meant to compute pairwise distances between + aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] + +unpack_options = '--strip-components=1' + +separate_build_dir = True + +buildininstalldir = True + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +build_cmd = ' make ' + +# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file +# will allways end up with /usr/local as the install prefix +install_cmd = 'mkdir -p %(installdir)s/bin &&' +install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' +install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' +install_cmd += ' %(installdir)s/bin ' + +sanity_check_paths = { + 'files': ['bin/tn93'], + 'dirs': [], +} + +sanity_check_commands = [ + 'tn93 -v', +] + +moduleclass = 'bio' From 8ecf6f50395db18b35f3391b79abe62f7b62e662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:15:54 +0100 Subject: [PATCH 474/528] no need to specify source_urls in matplotlib easyconfig, PythonPackage will automatically download from PyPI --- .../m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb index 57137691145..895aa8edc50 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', From 6088691847e431648f90ded6ba659d8a0772b87b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:31:37 +0100 Subject: [PATCH 475/528] set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with TensorFlow 2.5.0+ --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index a3949214369..b7a9a39b865 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -86,6 +86,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 9794ccd9035..c1662ad3a3b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index a364baf0775..18197cfebe6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), # Required for tensorboard_plugin_profile ('gviz-api', '1.9.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index 60b3de282bc..cb0493abde2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -84,6 +84,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), # Required for tensorboard_plugin_profile ('gviz-api', '1.9.0', { From 1aeacbefbe0db9bc848f8070283a3d7283457d42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:36:47 +0100 Subject: [PATCH 476/528] set for installing grcpio extension included with TensorFlow 2.2.3-2.4.1 with 2020* toolchain --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 1 + .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 1 + .../t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 9678677ff31..a41e6874956 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -95,6 +95,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 77a1ccd97e0..2cfb8444ca4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -86,6 +86,7 @@ exts_list = [ ('grpcio', '1.33.1', { 'modulename': 'grpc', 'checksums': ['f19782ec5104599382a0f73f2dfea465d0e65f6818bb3c49ca672b97034c64c3'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 1d255bd3b4b..5cae5dc8c13 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 2c463ccdf36..2342aee9b61 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -98,6 +98,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 34a3a4c37f9..ea58071275f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -99,6 +99,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', From eef1be11b8b794c86635011469b3008ede6eb1b2 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 15 Jan 2022 15:46:41 +0200 Subject: [PATCH 477/528] Remove incorrectly capitalized easyconfig --- .../t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb deleted file mode 100644 index e74ef4838b1..00000000000 --- a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Iñaki Mtz de Ilarduya Muñoz -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = "CMakeMake" - -name = 'tn93' -version = '1.0.7' - -homepage = 'https://github.com/veg/tn93' -description = """his is a simple program meant to compute pairwise distances between - aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] - -unpack_options = '--strip-components=1' - -separate_build_dir = True - -buildininstalldir = True - -builddependencies = [ - ('CMake', '3.20.1'), - ('binutils', '2.36.1'), -] - - -build_cmd = ' make ' - - -# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file -# will allways end up with /usr/local as the install prefix -install_cmd = 'mkdir -p %(installdir)s/bin &&' -install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' -install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' -install_cmd += ' %(installdir)s/bin ' - -sanity_check_paths = { - 'files': ['bin/tn93'], - 'dirs': [], -} - -moduleclass = 'bio' From 598fec56afb00d4fb4c74a956eaae5090413b96b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 16:16:44 +0100 Subject: [PATCH 478/528] update build dependencies for binutils 2.37 with system toolchain (fixes #14727) --- easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb | 29 +++++++++++++++++++ .../easyconfigs/b/binutils/binutils-2.37.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 4 +-- 3 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb new file mode 100644 index 00000000000..22f927345d6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' + +description = """ + Bison is a general-purpose parser generator that converts an annotated + context-free grammar into a deterministic LR or generalized LR (GLR) parser + employing LALR(1) parser tables. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb index b0741dccfc4..1a9094ebca7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.37.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb @@ -13,7 +13,7 @@ checksums = ['c44968b97cd86499efbc4b4ab7d98471f673e5414c554ef54afa930062dbbfcb'] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.6'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index 1beedb7a51c..16d474262c5 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -19,11 +19,11 @@ checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] # Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. # This results in not building man pages for the flex at SYSTEM level. builddependencies = [ - ('Bison', '3.5.3'), + ('Bison', '3.8.2'), ] dependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ] # glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct From 638677eeaebb88facb149cd2c7ed7b4925e88f26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 17:21:38 +0100 Subject: [PATCH 479/528] adding easyconfigs: CP2K-8.2-intel-2021a.eb, Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb, PLUMED-2.7.2-intel-2021a.eb --- .../c/CP2K/CP2K-8.2-intel-2021a.eb | 39 +++++++++++++ .../Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb | 44 +++++++++++++++ .../p/PLUMED/PLUMED-2.7.2-intel-2021a.eb | 56 +++++++++++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb new file mode 100644 index 00000000000..7db37eaa393 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '8.2' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2e24768720efed1a5a4a58e83e2aca502cd8b95544c21695eb0de71ed652f20a'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.1.5'), + ('libxsmm', '1.16.2'), + ('FFTW', '3.3.9'), + ('PLUMED', '2.7.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb new file mode 100644 index 00000000000..47c9ccee72c --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb @@ -0,0 +1,44 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', +] + +builddependencies = [ + ('Autotools', '20210128'), + ('GMP', '6.2.1'), + ('Boost', '1.76.0'), + ('Eigen', '3.3.9'), + ('Python', '2.7.18', '-bare'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb new file mode 100644 index 00000000000..fe971797a8e --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 3c6a9da7f95136df9b07caa4695b8b30fff50476 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 17:28:55 +0100 Subject: [PATCH 480/528] add GSL easyconfig that's required for PLUMED with intel-compilers/2021.2.0 --- .../g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..0466c9d75b8 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 397e8c675db268bee60eeb4b34e7c38be6696adc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:38:53 +0100 Subject: [PATCH 481/528] set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with Ray-project --- .../r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb | 1 + .../Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb index 6726bb26e7a..15d7ae893ef 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb @@ -75,6 +75,7 @@ exts_list = [ ('grpcio', '1.28.1', { 'modulename': 'grpc', 'checksums': ['cbc322c5d5615e67c2a15be631f64e6c2bab8c12505bc7c150948abdaa0bdbac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb index ea3efe2d1f9..90d60fc1d92 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb @@ -121,6 +121,7 @@ exts_list = [ ('grpcio', '1.33.2', { 'modulename': 'grpc', 'checksums': ['21265511880056d19ce4f809ce3fbe2a3fa98ec1fc7167dbdf30a80d3276202e'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], From 717d0940f621cdfb34370317a08ae6b865a09ce9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 15 Jan 2022 18:02:00 +0000 Subject: [PATCH 482/528] adding easyconfigs: wtdbg2-2.5-GCCcore-11.2.0.eb --- .../w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a3af9970a46 --- /dev/null +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu +# Updated to GCC 11.2.0 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'MakeCp' + +name = 'wtdbg2' +version = '2.5' + +homepage = 'https://github.com/ruanjue/wtdbg2' + +description = """ + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio + or Oxford Nanopore Technologies (ONT). It assembles raw reads without error + correction and then builds the consensus from intermediate assembly output. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/ruanjue/wtdbg2/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Perl', '5.34.0')] + +prebuildopts = "sed -i 's/CFLAGS=-g3/CFLAGS+=-g3/g' Makefile && " + +local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'pgzf'] + +files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts'], +} + +modextrapaths = { + 'PATH': 'scripts', +} + +moduleclass = 'bio' From 0be3abd726a247aa831904255c179833d1f006b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 Jan 2022 15:51:44 +0100 Subject: [PATCH 483/528] add sanity check command for wtdbg2 + ensure correct shebang in Perl scripts --- easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb index a3af9970a46..c9264b6e795 100644 --- a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb @@ -31,11 +31,15 @@ local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'p files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] +fix_perl_shebang_for = ['bin/*.pl', 'scripts/*.pl'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in local_executables], 'dirs': ['scripts'], } +sanity_check_commands = ["wtdbg2 --help"] + modextrapaths = { 'PATH': 'scripts', } From cd4bc87213c35242d82d8b495af1b1c72d36ff74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 Jan 2022 16:39:02 +0100 Subject: [PATCH 484/528] stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index d0148e063b5..8c61b1cbe83 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '15', '', True)] +dependencies = [('Java', '11', '', True)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." From d7fa762d5b3db5aec499261a310e68d99ccf3a43 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 17 Jan 2022 11:21:11 +0200 Subject: [PATCH 485/528] Rename the TN93 dependency on the hivtrace easyconfig --- easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index dc23ffb4a39..268a172e600 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), - ('tn93', '1.0.7'), + ('TN93', '1.0.7'), ('cURL', '7.76.0'), ('Pysam', '0.16.0.1'), ] From af9212fd05465cf7bedbef19d376fc2a0faf288f Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 17 Jan 2022 11:22:11 +0200 Subject: [PATCH 486/528] Remove options that are already defaults --- easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb index 4f9cb55bea9..91b0a720f20 100644 --- a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -18,19 +18,11 @@ source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] -unpack_options = '--strip-components=1' - -separate_build_dir = True - -buildininstalldir = True - builddependencies = [ ('CMake', '3.20.1'), ('binutils', '2.36.1'), ] -build_cmd = ' make ' - # this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file # will allways end up with /usr/local as the install prefix install_cmd = 'mkdir -p %(installdir)s/bin &&' From 741398e3ef869c055c55b12fbdade085bfe2bc52 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 17 Jan 2022 11:16:44 +0100 Subject: [PATCH 487/528] fix easybuild url in header/comments --- easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 2 +- easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index 268a172e600..5aeb814708a 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Iñaki Mtz de Ilarduya Muñoz # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb index 91b0a720f20..911f6914c26 100644 --- a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Iñaki Mtz de Ilarduya Muñoz # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics From 03f412eb5c6f2ae99d4af63374b90262eb7f6a3b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Jan 2022 12:01:27 +0100 Subject: [PATCH 488/528] Bump of nbconvert to version 6.4.0. The previous version, nbconvert 6.1.0, could cause permission denied errors when run in a shared environment. See https://github.com/jupyter/nbconvert/issues/1430 . This was fixed in PR https://github.com/jupyter/nbconvert/pull/1646 . Since many EasyBuild users work in shared environments, I think this is a relevant fix to have included. --- .../easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb index 27ff87d5da0..0ecf20cc339 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb @@ -90,8 +90,8 @@ exts_list = [ ('nbclient', '0.5.3', { 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], }), - ('nbconvert', '6.1.0', { - 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + ('nbconvert', '6.4.0', { + 'checksums': ['5412ec774c6db4fccecb8c4ba07ec5d37d6dcf5762593cb3d6ecbbeb562ebbe5'], }), ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], From 525c6d5c68c453fd5fa7bc631903b099e5abfabb Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Jan 2022 12:05:25 +0100 Subject: [PATCH 489/528] Also bump the version of nbconvert in IPython-7.26-0-GCCcore-11.2.0.eb --- .../easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb index 86c05a433f2..b8a2d71f584 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb @@ -90,8 +90,8 @@ exts_list = [ ('nbclient', '0.5.3', { 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], }), - ('nbconvert', '6.1.0', { - 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + ('nbconvert', '6.4.0', { + 'checksums': ['5412ec774c6db4fccecb8c4ba07ec5d37d6dcf5762593cb3d6ecbbeb562ebbe5'], }), ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], From 1f02a284fc2a7125b2065c32a0b7a7836c9e3f3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 17 Jan 2022 13:13:34 +0100 Subject: [PATCH 490/528] Newer CMake versions uses the cmake-config files from OS installed boost. Make sure it is not used when looking for the internally built boost. --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 2 ++ .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index 8e067a6bd05..edbae709f1c 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -51,6 +51,8 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb index 987778c4625..8d0eda20f5f 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb @@ -51,6 +51,8 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], From 34889831e29e5b6f962fcfa8dd3d39936f735e0b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 17 Jan 2022 13:11:13 +0000 Subject: [PATCH 491/528] adding easyconfigs: GTK+-3.24.31-GCCcore-11.2.0.eb --- .../g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bfa11921537 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.31' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.34.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('libepoxy', '1.5.8'), + ('X11', '20210802'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': [FTPGNOME_SOURCE], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' From cf0bacffd71cadaaf8793eb2f9e3201bdf6e5732 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Mon, 17 Jan 2022 15:31:57 +0100 Subject: [PATCH 492/528] Add patch for hard-coded checksum value of downloaded source file in the source code --- .../easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb | 6 +++++- .../RDKit-2021.03.4_fix-comic-neue-checksum.patch | 11 +++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb index 52be0571bb3..7535a3e2ace 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb @@ -13,10 +13,14 @@ toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} source_urls = ['https://github.com/rdkit/rdkit/archive/'] sources = ['Release_%s.tar.gz' % version.replace('.', '_')] -patches = ['RDKit-%(version)s_skip-broken-test.patch'] +patches = [ + 'RDKit-%(version)s_skip-broken-test.patch', + 'RDKit-2021.03.4_fix-comic-neue-checksum.patch', +] checksums = [ 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch + '80adeb72eb0e6fac3dcc6cca3c82c1a8fe253025106e0acb7b1135bc4b94a69d', # RDKit-2021.03.4_fix-comic-neue-checksum.patch ] # Dependencies varies from version to version diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch new file mode 100644 index 00000000000..de243222821 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch @@ -0,0 +1,11 @@ +--- rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt.orig 2022-01-17 13:56:43.780726092 +0100 ++++ rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt 2022-01-17 13:57:02.668646178 +0100 +@@ -12,7 +12,7 @@ + set(needDownload "FALSE") + endif() + if(needDownload) +- set(MD5Sum "23ed3f833c1ae0adb141a26b4a30d73e") ++ set(MD5Sum "850b0df852f1cda4970887b540f8f333") + downloadAndCheckMD5("https://fonts.google.com/download?family=Comic%20Neue" + "${CMAKE_CURRENT_SOURCE_DIR}/Comic_Neue.zip" + ${MD5Sum}) From 008e1773d9bb66759895eaa854723589e44e3bcb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jan 2022 17:25:40 +0200 Subject: [PATCH 493/528] add libaio.so.1 to libaio v0.3.112 --- .../l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb | 16 ++++++++++++---- .../l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb | 16 ++++++++++++---- .../l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb | 16 ++++++++++++---- 3 files changed, 36 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb index 699303eba68..1be5c814b95 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.35')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb index 076fa063db8..1ae85f5f820 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.36.1')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb index 2d6229d7fea..052974c15a8 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.37')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } From eb3a0e9b4e3a9e4c86f6e43e486c5dea20408b68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Jan 2022 19:22:29 +0100 Subject: [PATCH 494/528] add DSS extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 2725d3a7c9f..8227b4c8c80 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1078,6 +1078,12 @@ exts_list = [ ('ExomeDepth', '1.1.15', { 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], }), + ('bsseq', '1.30.0', { + 'checksums': ['2dada40e222d4f42510deeb99c24043078420a4d3d214d4cc3409d428cfb60c4'], + }), + ('DSS', '2.42.0', { + 'checksums': ['b1e2a9044cd10b09ecf667f7a3201269f2dca78ae431cccef6d46816e77dd1a8'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 1f8d5731fc9bdee49a9a127df2c4998dd158e018 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:35:39 +0100 Subject: [PATCH 495/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9706d2a7224..61b807a25db 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,7 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Max Voit -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'CAFE5' version = '5.0.0' From 22f94dc99221fbdb1be961597e839b0a19295411 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:36:09 +0100 Subject: [PATCH 496/528] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 61b807a25db..2f7bc2e4c96 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -25,7 +25,9 @@ sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' -install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' +with_configure = True +files_to_copy = ['bin', 'examples'] +postinstallcmds = ['chmod -x %(installdir)s/examples/*.txt'] sanity_check_paths = { 'files': ['bin/cafe5'], From fc613b43aa50e79dd1ed9bf7da6754dcd73d3063 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Jan 2022 09:35:40 +0100 Subject: [PATCH 497/528] add rpact and ldbounds extensions to R v4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index add27951e71..cdede914926 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3202,6 +3202,12 @@ exts_list = [ ('FactorCopula', '0.8', { 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], }), + ('rpact', '3.2.1', { + 'checksums': ['d12f9a085163a1745cc7672685dd24e04d27f76998a57835a1ea32e06b637471'], + }), + ('ldbounds', '1.1-1.1', { + 'checksums': ['e88e6bff43762a9f7d80484056d10c7d2fd80969b43061d8cc96c3bd5b9c3583'], + }), ] moduleclass = 'lang' From e7f05a0ecc69252c72814d571a7a71e23ac02819 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Jan 2022 10:25:10 +0000 Subject: [PATCH 498/528] Also apply bundle changes to FlexiBLAS w/ GCC 11.2.0 --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 31 ++++++++++++++++--- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index 24fbb34505e..cbaf8bd67aa 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'Bundle' + name = 'FlexiBLAS' version = '3.0.4' @@ -9,10 +11,6 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] - builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests @@ -33,4 +31,29 @@ backends = ['OpenBLAS', 'BLIS'] # if ARCH == 'x86_64': # backends.append('imkl') +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + moduleclass = 'lib' From 2e666c5ac7d64073a6c90d90e4fb51ddac7c0b46 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 11:37:07 +0100 Subject: [PATCH 499/528] update build dependencies for binutils 2.34, 2.35, 2.36.1 and GCCcore 9.3.0, 10.1.0, 10.2.0, 10.3.0 and 11.1.0 with system toolchain --- easybuild/easyconfigs/b/binutils/binutils-2.34.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.35.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34.eb index 1cf44b64555..a4138107365 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35.eb index 61d32277dde..5655c9dbc9e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.1'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb index 4b38ce2e34e..5f6e42bf744 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb @@ -13,7 +13,7 @@ checksums = ['e68edeaaeb6ca9687b6dcbaedd1b376506baad2d48de26a885fc5ab6acb839da'] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.6'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 8ea3bfbc136..757b0cd9eb8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -44,7 +44,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 98d75b65b5d..d4408b29aa0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -59,7 +59,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index b0e0681d116..e34ef9c9972 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -54,7 +54,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 072a64c40bb..b6a3f957cab 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -50,7 +50,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index 8870f60f1a2..6b1c47aa3c3 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -56,7 +56,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.34'), ] From d5108538e59e71d07f4fab328a8d0ec5d0440497 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 11:41:30 +0100 Subject: [PATCH 500/528] update build dependencies for GCCcore 9.4.0 with system toolchain --- easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb index aec0247b17e..c02024d4638 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb @@ -48,7 +48,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] From 13f8ccaf5d8e44bd89e1bc4e71b8864a275adbfd Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 11:11:39 +0000 Subject: [PATCH 501/528] Update FlexiBLAS-3.0.4-GCC-11.2.0.eb --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index cbaf8bd67aa..d84be83b2a1 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -26,10 +26,10 @@ dependencies = [ # note: first listed backend will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default -backends = ['OpenBLAS', 'BLIS'] +local_backends = ['OpenBLAS', 'BLIS'] # if ARCH == 'x86_64': -# backends.append('imkl') +# local_backends.append('imkl') default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} sanity_check_all_components = True @@ -40,6 +40,7 @@ components = [ 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + 'backends': local_backends, }), ('LAPACK', '3.10.0', { 'easyblock': 'CMakeMake', From ba11f6341ba894b6636b02b8d9109507dadcca32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 Jan 2022 12:24:41 +0100 Subject: [PATCH 502/528] make sure libxslt does not pick up OS installed libgcrypt or Python --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index 764ee9417e3..d17aa440dc4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb index 1fd2e54ea8a..121392cf7dc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb index 22a0c0a33e9..705654d4093 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index f3c2326d6f8..6097396bc50 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.9'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb index bc98e11869c..f414649f8fe 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], From 61e9d57b233b11c3aa82ea4ed1ce22a34d6eea55 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Jan 2022 11:50:17 +0000 Subject: [PATCH 503/528] Add test exception for bundles with per-component sanity checks --- test/easyconfigs/easyconfigs.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9360159096c..2e6d920d93e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -324,6 +324,8 @@ def check_dep_vars(self, gen, dep, dep_vars): if key not in retained_dep_vars: del dep_vars[key] + version_regex = re.compile('^version: (?P[^;]+);') + # filter out binutils with empty versionsuffix which is used to build toolchain compiler if dep == 'binutils' and len(dep_vars) > 1: empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] @@ -337,7 +339,7 @@ def check_dep_vars(self, gen, dep, dep_vars): for key in list(dep_vars): ecs = dep_vars[key] # filter out dep variants that are only used as dependency for parent with same version - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: dep_vars.pop(key) @@ -346,7 +348,7 @@ def check_dep_vars(self, gen, dep, dep_vars): for key in list(dep_vars): ecs = dep_vars[key] # filter out Boost variants that are only used as dependency for Boost.Python with same version - boost_ver = re.search('^version: (?P[^;]+);', key).group('ver') + boost_ver = version_regex.search(key).group('version') if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): dep_vars.pop(key) @@ -402,7 +404,7 @@ def check_dep_vars(self, gen, dep, dep_vars): dep = 'CUDA' for key in list(dep_vars): - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') # use version of Java wrapper rather than full Java version if dep == 'Java': dep_ver = '.'.join(dep_ver.split('.')[:2]) @@ -1018,6 +1020,8 @@ def test_pr_sanity_check_paths(self): # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + # also allow bundles that enable per-component sanity checks + bundle_sanity_check_components = ec.get('sanity_check_components') or ec.get('sanity_check_all_components') failing_checks = [] @@ -1028,6 +1032,8 @@ def test_pr_sanity_check_paths(self): if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass + elif easyblock == 'Bundle' and bundle_sanity_check_components: + pass else: ec_fn = os.path.basename(ec.path) failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) From 5fbba8eced5127c8b7c31f015a26aa3001e5557e Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 12:28:37 +0000 Subject: [PATCH 504/528] Update easyconfigs.py --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2e6d920d93e..be8299ccc06 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1020,8 +1020,6 @@ def test_pr_sanity_check_paths(self): # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] - # also allow bundles that enable per-component sanity checks - bundle_sanity_check_components = ec.get('sanity_check_components') or ec.get('sanity_check_all_components') failing_checks = [] @@ -1029,9 +1027,12 @@ def test_pr_sanity_check_paths(self): easyblock = ec.get('easyblock') + bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass + # also allow bundles that enable per-component sanity checks elif easyblock == 'Bundle' and bundle_sanity_check_components: pass else: From b342085f43e9151c719fcc182406467fde3b1e9e Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 12:31:36 +0000 Subject: [PATCH 505/528] linting --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index be8299ccc06..3659106ae97 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1028,7 +1028,7 @@ def test_pr_sanity_check_paths(self): easyblock = ec.get('easyblock') bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] - + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass From d73f326caa8fb7c143384f2b101c731b2a674c65 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 14:31:42 +0100 Subject: [PATCH 506/528] Added modextrapaths + fixed shebang for Python --- .../easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 20f3e803269..8e52500a1cf 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -28,15 +28,19 @@ dependencies = [ # remove included old GLPK copy postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] +fix_python_shebang_for = ['*.py'] + sanity_check_paths = { 'files': ['MinPath.py'], 'dirs': [], } sanity_check_commands = [ - "python3 MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", - "python3 MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", - "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", + "MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", ] +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From 1b51864209702dabf164546dcbc1f70507cfc980 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 Jan 2022 14:44:42 +0000 Subject: [PATCH 507/528] Conform to recent split of different GTK+ major release trees --- .../g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..016fad88acf --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.31' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.34.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('libepoxy', '1.5.8'), + ('X11', '20210802'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': [FTPGNOME_SOURCE], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' From cd024f505ad9c23b148c87ee6ee3452fca443411 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 Jan 2022 14:45:42 +0000 Subject: [PATCH 508/528] Delete GTK+-3.24.31-GCCcore-11.2.0.eb Remove badly named file --- .../g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb | 76 ------------------- 1 file changed, 76 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb deleted file mode 100644 index bfa11921537..00000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'Bundle' - -name = 'GTK+' -version = '3.24.31' - -homepage = 'https://developer.gnome.org/gtk3/stable/' -description = """GTK+ is the primary library used to construct user interfaces in GNOME. It - provides all the user interface controls, or widgets, used in a common - graphical application. Its object-oriented API allows you to construct - user interfaces without dealing with the low-level details of drawing and - device interaction. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -builddependencies = [ - ('binutils', '2.37'), - ('Autotools', '20210726'), - ('GObject-Introspection', '1.68.0'), - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), - ('cairo', '1.16.0'), - ('Perl', '5.34.0'), -] -dependencies = [ - ('ATK', '2.36.0'), - ('at-spi2-atk', '2.38.0'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.8'), - ('libepoxy', '1.5.8'), - ('X11', '20210802'), - ('FriBidi', '1.0.10'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCELOWER_TAR_XZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", - 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], - }), - ('hicolor-icon-theme', '0.17', { - 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], - 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], - }), - ('adwaita-icon-theme', '3.38.0', { - 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], - 'checksums': [ - '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', - # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch - 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', - ], - }), -] - -postinstallcmds = ['gtk-update-icon-cache'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', - 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', - 'gtk-update-icon-cache']] + - ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], - 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + - ['share/icons/hicolor', 'share/icons/Adwaita'], -} - - -moduleclass = 'vis' From bbfcdb49c516dcb2f22d0e357b97248adb731b32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jan 2022 16:14:44 +0100 Subject: [PATCH 509/528] adding easyconfigs: bcl2fastq2-2.20.0-GCC-11.2.0.eb --- .../bcl2fastq2-2.20.0-GCC-11.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..3843935b717 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + '%(name)s-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + '%(name)s-%(version)s-find-boost.patch', +] +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' From 09c2381a8a4183be49bf34397961c6652dd7581e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jan 2022 16:35:48 +0100 Subject: [PATCH 510/528] add comment to configopt --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb index 3843935b717..cbaad5ae5e9 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -51,6 +51,7 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { From be0006d48b55fcc3a68ccb3576feee4214860b6e Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 17:47:07 +0100 Subject: [PATCH 511/528] Fixed error + edited patch desc --- .../Short-Pair-20170125-Python3fix.patch | 3 ++- .../Short-Pair/Short-Pair-20170125-foss-2021b.eb | 15 +++++---------- 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch index 4c5da5540cd..75fc857ea70 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch @@ -1,5 +1,6 @@ Makes Short-Pair compatible with Phyton3 -Author: Filip Kružík (INUITS) +Created by using already existing version of file from github.com/jtamames/SqueezeMeta (commit 68f8581eef7eb34ffb28ef412fdce1ebf20244b6) +Patch created by: Filip Kružík (INUITS) --- Short-Pair_fix 2022-01-11 17:08:22.763000000 +0100 +++ Short-Pair.py 2022-01-11 17:05:28.709307000 +0100 @@ -1,4 +1,4 @@ diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb index 8fd96339019..40a6651c00a 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -10,9 +10,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [SOURCEFORGE_SOURCE] sources = [{'download_filename': 'Short-Pair.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3'] - patches = ['Short-Pair-20170125-Python3fix.patch'] +checksums = [ + 'c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3', # Short-Pair-20170125.tar.gz + '71f53bea8d1056abf22d35bdb8b87f41fa1482dd4b402e788dbd536e0f6408c0', # Short-Pair-20170125-Python3fix.patch +] dependencies = [ ('Python', '3.9.6'), @@ -20,13 +22,6 @@ dependencies = [ ('SciPy-bundle', '2021.10') ] -exts_list = [ - ('numpy', '1.22.0', { - 'source_urls': ['https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/'], - 'sources': ['%(name)s-%(version)s.zip'], - }) -] - cmds_map = [('.*', "$CXX $CXXFLAGS -w -o DNA2Protein DNA2Protein.cpp")] files_to_copy = [(['DNA2Protein', 'get_hmm.sh', 'hmmer3_pipeline_missing_end.sh', 'Short-Pair.py'], 'bin')] @@ -42,6 +37,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["python3 bin/Short-Pair.py -h"] +sanity_check_commands = ["bin/Short-Pair.py -h"] moduleclass = 'bio' From 6e8dc42e9257a6872a7d3e2c764345a4acc63659 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 19:00:03 +0200 Subject: [PATCH 512/528] fix CVE-2021-23437 in Pillow v7 and v8 --- .../matplotlib/matplotlib-3.4.3-foss-2021b.eb | 2 +- .../matplotlib-3.4.3-intel-2021b.eb | 2 +- ...Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 6 +++- .../p/Pillow/Pillow-7_CVE-2021-23437.patch | 27 ++++++++++++++++ .../p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 6 +++- .../p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 6 +++- .../p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 6 +++- .../p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ .../p/Pillow/Pillow-8_CVE-2021-23437.patch | 30 +++++++++++++++++ 9 files changed, 111 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb index 5eefa7f3e9c..735ad398a7d 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '8.3.1'), + ('Pillow', '8.3.2'), ('Qhull', '2020.2') ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb index 51d59ef7c45..2561f744e68 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '8.3.1'), + ('Pillow', '8.3.2'), ('Qhull', '2020.2') ] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index 51e4a86a83a..9fc85ff2e06 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -11,7 +11,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '9.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946', # Pillow-7.0.0.tar.gz + '8c4195792e3a3581fef80a4cbca39f1123c0b83f74acc002bbbec7185c62baf3', # Pillow-7_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch new file mode 100644 index 00000000000..747c20f3ae8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch @@ -0,0 +1,27 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +--- a/src/PIL/ImageColor.py 2020-01-02 09:31:35.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2022-01-18 16:42:11.359922625 +0100 +@@ -32,6 +32,8 @@ + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +--- a/Tests/test_imagecolor.py 2022-01-18 16:42:11.362700436 +0100 ++++ b/Tests/test_imagecolor.py 2022-01-18 17:43:53.880517448 +0100 +@@ -182,3 +182,11 @@ + self.assertEqual((255, 255), ImageColor.getcolor("white", "LA")) + self.assertEqual((163, 33), ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA")) + Image.new("LA", (1, 1), "white") ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 9304f308f90..bff212b445d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 198aa646f08..eca48ea8134 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1', # Pillow-8.2.0.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 32bbaf622c5..3d455621b67 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792', # Pillow-8.3.1.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9567cc977dd --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '8.3.2' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dde3f3ed8d00c72631bc19cbfff8ad3b6215062a5eed402381ad365f82f0c18c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch new file mode 100644 index 00000000000..57504df710a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch @@ -0,0 +1,30 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +diff -rupN --no-dereference Pillow-8.1.2/src/PIL/ImageColor.py Pillow-8.1.2-new/src/PIL/ImageColor.py +--- a/src/PIL/ImageColor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -32,6 +32,8 @@ def getrgb(color): + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +diff -rupN --no-dereference Pillow-8.1.2/Tests/test_imagecolor.py Pillow-8.1.2-new/Tests/test_imagecolor.py +--- a/Tests/test_imagecolor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/Tests/test_imagecolor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -191,3 +191,12 @@ def test_rounding_errors(): + assert (255, 255) == ImageColor.getcolor("white", "LA") + assert (163, 33) == ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA") + Image.new("LA", (1, 1), "white") ++ ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) From 071d475a7d21c3c0c9b6f105c26503865b902644 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 18:22:44 +0100 Subject: [PATCH 513/528] Added required changes + patched DAS_Tool to work with BLAST+ by default --- ...AS_Tool-1.1.1-deafaultSearchEngBLAST.patch | 23 +++++++ .../DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 11 ++- .../r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 67 +++++++++---------- 3 files changed, 64 insertions(+), 37 deletions(-) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch new file mode 100644 index 00000000000..6a99fcf0345 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch @@ -0,0 +1,23 @@ +Because we are not using USEARCH, this patch will set deafult search engine to used BLAST+ +Author: Filip Kružík (INUITS) + +--- DAS_Tool.orig 2022-01-18 16:13:32.781571000 +0100 ++++ DAS_Tool 2022-01-18 16:15:43.039420000 +0100 +@@ -52,7 +52,7 @@ + echo " -o, --outputbasename Basename of output files." + echo " -l, --labels Comma separated list of binning prediction names. (optional)" + echo " --search_engine Engine used for single copy gene identification [blast/diamond/usearch]." +- echo " (default: usearch)" ++ echo " (default: blast)" + echo " --write_bin_evals Write evaluation for each input bin set [0/1]. (default: 1)" + echo " --create_plots Create binning performance plots [0/1]. (default: 1)" + echo " --write_bins Export bins as fasta files [0/1]. (default: 0)" +@@ -117,7 +117,7 @@ + create_plots=1 + write_bins=0 + write_unbinned=0 +-search_engine="usearch" ++search_engine="blast" + b_weight=0.6 + c_weight=0.5 + db_dir=$DIR\/db diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb index 81cc573725f..cd27a7c4c28 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] +patches=['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +checksums = [ + '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch +] dependencies = [ ('R', '4.1.2'), @@ -27,10 +31,10 @@ exts_defaultclass = 'RPackage' exts_list = [ (name, version, { + 'modulename': 'DASTool', 'source_tmpl': 'DASTool_%(version)s.tar.gz', 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], - 'modulename': 'DASTool', }), ] @@ -44,10 +48,11 @@ sanity_check_paths = { 'dirs': ['DASTool/R'], } +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] #Help gets printed correctly, but the error code is 1 + modextrapaths = { 'PATH': '', 'R_LIBS_SITE': '', } - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb index 6e37c235463..e415e258542 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -24,20 +24,20 @@ exts_default_options = { # each version is picked as high as possible to fullfill all requirements # packages updated on 2021-07-02 exts_list = [ - ('ffi', '1.15.3', { - 'checksums': ['98d5c5c4281c9c0466acc60cf0e79124bf3c311417fd97e7473e41722953fbf1'], + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], }), ('childprocess', '4.1.0', { 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], }), - ('json', '2.5.1', { - 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + ('json', '2.6.1', { + 'checksums': ['7ff682a2db805d6b924e4e87341c3c0036824713a23c58ca53267ce7e5ce2ffd'], }), ('cabin', '0.9.0', { 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], }), - ('backports', '3.21.0', { - 'checksums': ['f9394457cb1dd5ca1b7bdc0dfbbd8f56f5cde40f45f96bc90f0f895a87e41b77'], + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], }), ('arr-pm', '0.0.11', { 'checksums': ['f1ab088421276f446da1971c5071defd1504855ec46e196815fa43cd62d61a9f'], @@ -48,17 +48,17 @@ exts_list = [ ('multipart-post', '2.1.1', { 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], }), - ('ruby2_keywords', '0.0.4', { - 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], }), - ('faraday-net_http', '1.0.1', { - 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + ('faraday-net_http', '2.0.1', { + 'checksums': ['f867b028552c3cf018b9293b58b993dc238ba62683568b3e194c673afe62d700'], }), - ('faraday', '1.3.0', { - 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + ('faraday', '1.0.0', { + 'checksums': ['e67631809ae5633a1d2b03adfa83939a91a095f6dc61a1f322826612613dd687'], }), - ('faraday_middleware', '1.0.0', { - 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], }), ('highline', '2.0.3', { 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], @@ -78,17 +78,17 @@ exts_list = [ ('public_suffix', '4.0.6', { 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], }), - ('addressable', '2.7.0', { - 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + ('addressable', '2.8.0', { + 'checksums': ['f76d29d2d1f54b6c6a49aec58f9583b08d97e088c227a3fcba92f6c6531d5908'], }), ('concurrent-ruby', '1.1.9', { 'checksums': ['0ec0846d991c38f355b4228ad8ea77aa69c3fdaa320cd574dafedc10c4688a5b'], }), - ('i18n', '1.8.10', { - 'checksums': ['ca24e52fdd6ad7af419241eef8c41e65ef4e3499c6b252df13f697919eb24e3c'], + ('i18n', '1.8.11', { + 'checksums': ['ae133354590b49070b87c83f8fe8cc064ffdc40ca76364535e100312e30cad6d'], }), - ('minitest', '5.14.4', { - 'checksums': ['f4716634d71b3ffb627cd63ba4f6f0f77c7a3f17353b1bdf52c8a7f2e0e4e7a7'], + ('minitest', '5.15.0', { + 'checksums': ['6d2d5bfa301257ef2c2fe8818abeaa0932ed54735c8ed039459cb4f85029ae1b'], }), ('thread_safe', '0.3.6', { 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], @@ -96,11 +96,11 @@ exts_list = [ ('tzinfo', '1.1.0', { 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], }), - ('zeitwerk', '2.4.2', { - 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + ('zeitwerk', '2.5.3', { + 'checksums': ['ddfeb36d24444b10f402cae2ee5a05c580f54115ae25bcf2ac29bf814c4faf52'], }), - ('activesupport', '5.0.7.2', { - 'checksums': ['f75cc67fb08421bdf4c2a383a47d9b3b02ce5eec4749704b1286fb0c12c98bad'], + ('activesupport', '5.2.6', { + 'checksums': ['7249ee13859fc99ed2c833048674fd28c11605c679f1c65035190a2219e9cbef'], }), ('gh', '0.18.0', { 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], @@ -108,8 +108,8 @@ exts_list = [ ('launchy', '2.5.0', { 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], }), - ('ethon', '0.14.0', { - 'checksums': ['10e267a39d7e2a92d944e5681ba46dbd211b5b5b6cf9b51afb769b8417247ead'], + ('ethon', '0.15.0', { + 'checksums': ['0809805a035bc10f54162ca99f15ded49e428e0488bcfe1c08c821e18261a74d'], }), ('typhoeus', '1.4.0', { 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], @@ -120,11 +120,11 @@ exts_list = [ ('pusher-client', '0.6.2', { 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], }), - ('diff-lcs', '1.4.4', { - 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], }), - ('rspec-support', '3.10.2', { - 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + ('rspec-support', '3.10.3', { + 'checksums': ['65c88f8cbe579461f411097682e6402960eae327eef08e86ef581b8c609e4c5e'], }), ('rspec-mocks', '3.10.2', { 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], @@ -156,9 +156,8 @@ exts_list = [ ('rack-test', '1.1.0', { 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], }), - ('bundler', '2.2.21', { - 'checksums': ['3c8dc5e0cf66d385a9b33751e54986290d42023c5e1bba2b5df094917b6e234a'], - }), -] + ('bundler', '2.3.5', { + 'checksums': ['2553cbd138b466bc56a3c724c5c28648dff8e2343b13a7c696cf9c2818c8d629'], + }),] moduleclass = 'lang' From 70f4ad2087effcb61d8fc75b90d5ce5f199d213c Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 19:10:08 +0100 Subject: [PATCH 514/528] Fixed style errors --- .../d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb index cd27a7c4c28..4e04c72ff76 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] -patches=['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] checksums = [ '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch @@ -48,7 +48,8 @@ sanity_check_paths = { 'dirs': ['DASTool/R'], } -sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] #Help gets printed correctly, but the error code is 1 +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] +# Help gets printed correctly, but the error code is 1 modextrapaths = { 'PATH': '', From 7abc08ef69de88a00fa1ddf0b86b31f145a34909 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 20:26:28 +0200 Subject: [PATCH 515/528] fix checksum of Pillow-8_CVE-2021-23437.patch --- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index bff212b445d..7bdf2476477 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index eca48ea8134..42cbf229337 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ 'a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1', # Pillow-8.2.0.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 3d455621b67..a9516e2ab73 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ '2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792', # Pillow-8.3.1.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.37')] From a9fdde4f6c3610e8b8038b7a8b03c5033626e491 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 19:36:47 +0100 Subject: [PATCH 516/528] Another style fix --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb index e415e258542..dc6ba8f38af 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -158,6 +158,6 @@ exts_list = [ }), ('bundler', '2.3.5', { 'checksums': ['2553cbd138b466bc56a3c724c5c28648dff8e2343b13a7c696cf9c2818c8d629'], - }),] + })] moduleclass = 'lang' From 4a48c4a5338d8a652baba6058a9fb06f448e22fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jan 2022 08:32:05 +0100 Subject: [PATCH 517/528] fix typo --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb index cbaad5ae5e9..5369e23685c 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -51,7 +51,7 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' -# Make sure CMake doesn't use any system install Boost versions cmake-config files. +# Make sure CMake doesn't use any system installed Boost versions cmake-config files. configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { From b7b2f1bf96463fb92c83c4fc23a7022f9f75778a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Jan 2022 08:49:29 +0100 Subject: [PATCH 518/528] only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3659106ae97..89afb89a610 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1024,18 +1024,20 @@ def test_pr_sanity_check_paths(self): failing_checks = [] for ec in self.changed_ecs: - easyblock = ec.get('easyblock') + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): - bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] + sanity_check_ok = False - if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): - pass + sanity_check_ok = True + # also allow bundles that enable per-component sanity checks - elif easyblock == 'Bundle' and bundle_sanity_check_components: - pass - else: + elif easyblock == 'Bundle': + if ec['sanity_check_components'] or ec['sanity_check_all_components']: + sanity_check_ok = True + + if not sanity_check_ok: ec_fn = os.path.basename(ec.path) failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) From e6432c4eeb153145388a1f32a64803dfc1ed46a5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 19 Jan 2022 12:01:11 +0000 Subject: [PATCH 519/528] Update easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb Update `adwaita-icon-theme` and fix URL Co-authored-by: Alex Domingo --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb index 016fad88acf..f4bdb729cdb 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb @@ -49,12 +49,12 @@ components = [ 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), - ('adwaita-icon-theme', '3.38.0', { + ('adwaita-icon-theme', '40.1.1', { 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], 'checksums': [ - '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + '0b6c436ed6ad9887a88ada1f72a0197b1eb73b020d8d344abab4c7fa7250f8f6', # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', ], From 70bfefbaca3fbbfcbbf3792ada7366270e3f36be Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 19 Jan 2022 16:37:32 +0100 Subject: [PATCH 520/528] Added required changes --- .../s/Short-Pair/Short-Pair-20170125-foss-2021b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb index 40a6651c00a..5e21f81106f 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -30,13 +30,11 @@ fix_python_shebang_for = ['bin/Short-Pair.py'] postinstallcmds = ["chmod a+rx %(installdir)s/bin/*"] -exts_defaultclass = 'PythonBundle' - sanity_check_paths = { 'files': ['bin/DNA2Protein', 'bin/get_hmm.sh', 'bin/hmmer3_pipeline_missing_end.sh', 'bin/Short-Pair.py'], 'dirs': [], } -sanity_check_commands = ["bin/Short-Pair.py -h"] +sanity_check_commands = ["Short-Pair.py -h"] moduleclass = 'bio' From 9e333911ca70d4cac60002fcacec64916ace3d33 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jan 2022 16:36:06 +0000 Subject: [PATCH 521/528] fix CVE-2021-23437 in Pillow-SIMD v8 + add Pillow-SIMD v8.3.2 in easyconfigs using a 2021b toolchain --- .../Pillow-SIMD/Pillow-8_CVE-2021-23437.patch | 30 ++++++++++++++ .../Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb | 6 ++- .../Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb | 6 ++- .../Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 4 files changed, 79 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch new file mode 100644 index 00000000000..57504df710a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch @@ -0,0 +1,30 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +diff -rupN --no-dereference Pillow-8.1.2/src/PIL/ImageColor.py Pillow-8.1.2-new/src/PIL/ImageColor.py +--- a/src/PIL/ImageColor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -32,6 +32,8 @@ def getrgb(color): + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +diff -rupN --no-dereference Pillow-8.1.2/Tests/test_imagecolor.py Pillow-8.1.2-new/Tests/test_imagecolor.py +--- a/Tests/test_imagecolor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/Tests/test_imagecolor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -191,3 +191,12 @@ def test_rounding_errors(): + assert (255, 255) == ImageColor.getcolor("white", "LA") + assert (163, 33) == ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA") + Image.new("LA", (1, 1), "white") ++ ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb index 07c0c7e731c..23fe713f7d7 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['d966a27bd027d960c62ce5593858b4bf3e98ea44b9f7684a4486086b6f0ea3aa'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'd966a27bd027d960c62ce5593858b4bf3e98ea44b9f7684a4486086b6f0ea3aa', # 8.2.0.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb index 9b2bde2adbc..74b967e8926 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['bf77f392094e3bb24ca56ef8bbc4ea0d9752226ff348682d849c0aa8c1577980'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'bf77f392094e3bb24ca56ef8bbc4ea0d9752226ff348682d849c0aa8c1577980', # 8.3.1.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cea197aa05e --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '8.3.2' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['095bcf74c6e4d36e1e1ff2d7926b83169f0dc29bb6731734c39d3c9522ae81b2'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From c2f8c0ee7ccdc77f83594ac8d3929f923aec4e27 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jan 2022 17:15:45 +0000 Subject: [PATCH 522/528] the Pillow v8 patch also works for Pillow-SIMD v7 --- .../p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb | 6 +++++- .../Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb index 712cf054a06..9c4aa141b7c 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] +patches = ['Pillow-8_CVE-2021-23437.patch'] +checksums = [ + '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb index fd8571b95b9..0faafe7a94a 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] +patches = ['Pillow-8_CVE-2021-23437.patch'] +checksums = [ + '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.34')] From 1c52b44bf3753f2427bf21e7eddeeeb5f84fdfae Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Thu, 20 Jan 2022 08:14:59 +0100 Subject: [PATCH 523/528] Update RDKit-2021.03.4: add comic-neue-checksum patch description and author --- .../r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch index de243222821..3316f1a811c 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch @@ -1,3 +1,9 @@ +As part of its installation, RDKit downloads a font package from https://fonts.google.com +and checks its md5sum. It appears the font package was modified and therefore a new md5sum +must be used. The authors of RDKit have updated the md5sum in the source code of RDKit but +no backward fix was made for already existing releases. This patch updates the md5 checksum +to the its new value. +Author: Robin Engler, SIB Swiss Institute for Bioinformatics --- rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt.orig 2022-01-17 13:56:43.780726092 +0100 +++ rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt 2022-01-17 13:57:02.668646178 +0100 @@ -12,7 +12,7 @@ From 33c378c1be0bc3c6d34b7eb29409190865571cf3 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Thu, 20 Jan 2022 08:41:04 +0100 Subject: [PATCH 524/528] Update RDKit-2021.03.4: update comic-neue-checksum patch checksum --- easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb index 7535a3e2ace..3146628e323 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch - '80adeb72eb0e6fac3dcc6cca3c82c1a8fe253025106e0acb7b1135bc4b94a69d', # RDKit-2021.03.4_fix-comic-neue-checksum.patch + '64d2c588203998c1da028b95032a7c006834e957f10c6335bb534148c0517dcb', # RDKit-2021.03.4_fix-comic-neue-checksum.patch ] # Dependencies varies from version to version From bbfa623c8c96a00158f25293509449351780e24c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Jan 2022 19:09:53 +0100 Subject: [PATCH 525/528] add pathview extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 8227b4c8c80..53b854a4603 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1084,6 +1084,9 @@ exts_list = [ ('DSS', '2.42.0', { 'checksums': ['b1e2a9044cd10b09ecf667f7a3201269f2dca78ae431cccef6d46816e77dd1a8'], }), + ('pathview', '1.34.0', { + 'checksums': ['594e4b2dd4bb9e826fa87c63f56fbc9132e1b4b620696ec31ae0ebbc6940b4c9'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 9390faedad5c8704cc544094aebcbe32657164f9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Jan 2022 15:01:27 +0000 Subject: [PATCH 526/528] add libXfont2 patch to fix build when libbsd is present --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 7 ++++- .../x/X11/X11-20210518-GCCcore-10.3.0.eb | 7 ++++- .../x/X11/libXfont2-2.0.4_libbsd.patch | 26 +++++++++++++++++++ 3 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index 041c9f6a6a9..d1a9f51ec07 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -126,7 +126,12 @@ components = [ 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], }), ('libXfont2', '2.0.4', { # 2019-09-14 - 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + 'patches': ['libXfont2-2.0.4_libbsd.patch'], + 'checksums': [ + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '5c8d51f9e65d4e9f49c0fb5f82cfbf87b3cf02f67c1dacf6521a56d8ffb1ae91', # libXfont2-2.0.4_libbsd.patch + ], + 'preconfigopts': "autoreconf -i && ", }), ('libXft', '2.3.3', { # 2019-03-16 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], diff --git a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb index 508c2e2c167..b2104033854 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb @@ -126,7 +126,12 @@ components = [ 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], }), ('libXfont2', '2.0.4', { # 2019-09-14 - 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + 'patches': ['libXfont2-2.0.4_libbsd.patch'], + 'checksums': [ + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '5c8d51f9e65d4e9f49c0fb5f82cfbf87b3cf02f67c1dacf6521a56d8ffb1ae91', # libXfont2-2.0.4_libbsd.patch + ], + 'preconfigopts': "autoreconf -i && ", }), ('libXft', '2.3.3', { # 2019-03-16 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], diff --git a/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch b/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch new file mode 100644 index 00000000000..19684aea813 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch @@ -0,0 +1,26 @@ +From ce7a3265019e4d66198c1581d9e8c859c34e8ef1 Mon Sep 17 00:00:00 2001 +From: Bernd Kuhls +Date: Sat, 19 Oct 2019 09:32:41 +0200 +Subject: [PATCH] configure: define HAVE_LIBBSD when libbsd was found + +--- + configure.ac | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/configure.ac b/configure.ac +index e497325..d4d8aa4 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -53,6 +53,9 @@ AC_CHECK_HEADERS([endian.h poll.h sys/poll.h]) + # Checks for library functions. + AC_CHECK_FUNCS([poll readlink]) + AC_SEARCH_LIBS([strlcat], [bsd]) ++if test "$ac_cv_search_strlcat" = "-lbsd"; then ++ AC_DEFINE(HAVE_LIBBSD,1,[Has libbsd]) ++fi + AC_CONFIG_LIBOBJ_DIR([src/util]) + AC_REPLACE_FUNCS([reallocarray realpath strlcat strlcpy]) + +-- +GitLab + From 0a205792b7e5bd849d0cd6cf0d97271adee4392d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 22 Jan 2022 15:27:05 +0800 Subject: [PATCH 527/528] prepare release notes for EasyBuild v4.5.2 + bump version to 4.5.2 --- RELEASE_NOTES | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e4cfd357446..24bac8fac8f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,67 @@ The latest version of easybuild-easyconfig provides 13,812 easyconfig files, for incl. 36 different (compiler) toolchains. +v4.5.2 (January 24th 2022) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 48 new software packages: + - alevin-fry (#14617), AMD-uProf (#14626), ANGEL (#11857), atropos (#7580), Austin (#14596), AutoDock-GPU (#14671), + AutoDock-Vina (#14675), boost_histogram (#14516), CAFE5 (#14603), Calcam (#7488), Carma (#14527), Cogent (#14278), + dlib (#14556), DualSPHysics (#14632), dune-core (#14693), dune-fem (#14693), DyMat (#14615), elbencho (#14548), + Embree (#7471), ExaML (#14530), FMPy (#14481), genozip (#14583), hivtrace (#14691), intervaltree-python (#8995), + IsoNet (#14075), MACSE (#14709), MetaPhlAn (#12917), MicrobeAnnotator (#14549), mold (#14595), numdiff (#14609), + OpenFace (#14556), PhyloPhlAn (#14564), PREQUAL (#14722), PuLP (#14581), PyCalib (#14616), PyTorch3D (#13240), + QCG-PilotJob (#14337), RaGOO (#8995), RAPSearch2 (#13199), SCopeLoomR (#14518), ShengBTE (#14557), SHTns (#14682), + STRUMPACK (#14560), TALYS (#14716), TN93 xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) +- added additional easyconfigs for various supported software packages, including: + - AdapterRemoval 2.3.2, alevin fry, AMD uProf, AMOS 3.1.0, Anaconda3 2021.11.eb, ANGEL 3.0, annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, arpack ng, Arrow 0.17.1, Arrow 6.0.1, atropos 1.1.21, Austin 3.2.0, Austin 3.2.0.eb, AutoDock 4.2.6, AutoDock GPU, AutoDock Vina, AutoDock Vina, Bazel 3.7.2, bcl2fastq2 2.20.0, Bismark 0.23.1, Bison 3.8.2.eb, BLAST+ 2.12.0, Blender 3.0.0, boost_histogram 1.2.1, Bowtie2 2.4.4, BWA 0.7.17, CAFE5 5.0.0, Calcam 2.1.0, Calcam 2.1.0, canu 2.2, Carma 2.01, CD HIT, cDNA_Cupcake 24.2.0, cDNA_Cupcake 26.0.0, CDO 1.9.10, CGAL 4.14.3, CheckM 1.1.3, CHERAB 1.3.0, CHERAB 1.3.0, CMake 3.20.1, CMake 3.22.1, Cogent 8.0.0, CompareM 0.1.2, CP2K 8.2, CUDAcore 11.4.0.eb, CVXOPT 1.2.3, Cython 3.0a5, DAS_Tool 1.1.1, DendroPy 4.5.2, DIAMOND 2.0.13, DIAMOND 2.0.13, dill 0.3.4, dlib 19.22, dlib 19.22, dotNET Core, dotNET SDK, DualSPHysics 5.0.175, DualSPHysics 5.0.175, dune core, dune fem, DyMat 0.7, EasyBuild 4.5.1.eb, Eigen 3.4.0, EIGENSOFT 7.2.1, elbencho 2.0, ELSI RCI, ELSI RCI, ELSI RCI, ELSI RCI, Embree 3.4.0, ExaML 3.0.22, expecttest 0.1.3, Extrae 3.8.3, fastp 0.23.2, FastTree 2.1.11, FMPy 0.3.2, FragGeneScan 1.31, FreeImage 3.18.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FTGL 2.1.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, gengetopt 2.23, genozip 13.0.5, georges 2019.2, GffCompare 0.12.6, gffread 0.12.7, gffread 0.12.7, gmsh 4.9.0, gnuplot 5.4.2, graphite2 1.3.14, GSL 2.7, GTDB Tk, GTK3 3.24.31, h5py 3.6.0, h5py 3.6.0, hivtrace 0.6.2, HMMER 3.3.2, Horovod 0.23.0, HPL 2.3, hypothesis 4.57.1, IDBA UD, igraph 0.9.5, iimpi 2022.00.eb, imkl 2022.0.1.eb, imkl FFTW, impi 2021.5.0, Inspector 2022.0.0.eb, intel 2022.00.eb, intel compilers, intervaltree python, IPython 5.10.0, IQ TREE, ISA L, IsoNet 0.1_20210822_04_674f67f, itac 2021.2.0.eb, itac 2021.5.0.eb, Java 15.0.1.eb, Java 15.eb, Java 17.0.1.eb, Java 17.eb, Java 1.8.0_311.eb, JUBE 2.4.2.eb, Julia 1.6.5, Julia 1.7.1, Kaleido 0.2.1, KronaTools 2.8.1, leidenalg 0.8.8, libdeflate 1.8, libdwarf 20210305, libelf 0.8.13, libgd 2.3.3, Libint 2.6.0, libxsmm 1.17, LMfit 1.0.3, LSD2 2.3, MACSE 2.06, MAGMA 1.09b, mapDamage 2.2.1, MATLAB 2021b.eb, matplotlib 2.2.5, MaxBin 2.2.7, MEGAHIT 1.2.9, MetaBAT 2.15, MetaPhlAn 3.0.9, MicrobeAnnotator 2.0.5, MinPath 1.6, mold 0.9.6, mold 1.0.0, molmod 1.4.8, MultiQC 1.10.1, MultiQC 1.11, MUMmer 4.0.0beta2, MUSCLE 3.8.31, MUSCLE 3.8.31, MUSCLE 5.0.1428, ncview 2.1.8, NGS Python, numba 0.50.1, numba 0.54.1, numdiff 5.9.0, NVHPC 21.11.eb, OBITools 1.2.13, occt 7.5.0p1, OpenBabel 3.1.1, openCARP 8.2, OpenCV 3.4.1, OpenFace 2.2.0, OpenFace 2.2.0, OpenFOAM v2112, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, PAML 4.9j, parasail 2.4.3, ParaView 5.9.1, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, PEAR 0.9.11, phonopy 2.12.0, PhyloPhlAn 3.0, PhyloPhlAn 3.0.2, Pillow 8.3.2, Pillow SIMD, plotly.py 4.14.3, PLUMED 2.7.2, PLUMED 2.7.3, poppler 22.01.0, PREQUAL 1.02, PRINSEQ 0.20.4, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, pullseq 1.0.2, PuLP 2.5.1, pybind11 2.7.1, PyCairo 1.20.1, PyCalib 0.1.0.dev0, PyOpenCL 2021.1.2, PyOpenGL 3.1.5, PyQt5 5.9.2, PyQtGraph 0.12.3, Python 2.7.18, python igraph, python parasail, PyTorch 1.10.0, PyTorch3D 0.4.0, PyZMQ 22.3.0, QCG PilotJob, Qt5 5.15.2, RaGOO 1.11, RAPSearch2 2.24, RAxML 8.2.12, Raysect 0.7.1, Raysect 0.7.1, RDP Classifier, Rgurobi 9.5.0, Ruby 3.0.1, scanpy 1.8.2, Schrodinger 2021, SciPy bundle, SCopeLoomR 0.13.0, SCOTCH 6.1.2, SEPP 4.3.10, SEPP 4.5.0, SEPP 4.5.1, seqtk 1.3, ShengBTE 1.1.1, Short Pair, SHTns 2.7, SHTns 3.5.1, SIP 4.19.8, Spack 0.17.0.eb, SPAdes 3.15.3, Spark 3.1.1, SqueezeMeta 1.0.0, STAR 2.7.9a, statsmodels 0.13.1, statsmodels 0.13.1, STRUMPACK 6.1.0, STRUMPACK 6.1.0, Subread 2.0.3, SuiteSparse 5.10.1, TALYS 1.95, TALYS 1.95, texlive 20210324, Tkinter 2.7.18, TN93 1.0.7, TreeMix 1.13, trimAl 1.4.1, VCFtools 0.1.16, VTune 2022.0.0.eb, worker 1.6.12, wtdbg2 2.5, XML LibXML, xxHash 0.8.0, yaff 1.6.0, yaml cpp, Zgoubi 6.0.2 +- minor enhancements, including: + - add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (#14547) + - include output of failing code style check in message produced by failing easyconfigs style test (#14578) + - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591) + - add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig (#14634) + - add FactorCopula extension for R v4.1.2 (#14648) + - add ExomeDepth extension to R-bundle-Bioconductor 3.14 (#14684) + - add DSS extension to R-bundle-Bioconductor 3.14 (#14748) + - add rpact and ldbounds extensions to R v4.1.2 (#14750) + - add pathview extension to R-bundle-Bioconductor 3.14 (#14806) +- various bug fixes, including: + - fix homepage and source_urls for GLIMMER 3.02b (#7945) + - use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (#14565) + - fix checksum and versions of annovar v20191024 (#14579) + - add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (#14584) + - retain version in filename for cromwell sources (#14586) + - specify compiler to use in WildMagic easyconfig (#14594) + - avoid need for git build dependency for recent x265 easyconfigs (#14605) + - fix broken patch file for recent GPAW versions (#14619) + - add alternative checksum for Siesta-4.1-MaX-1.0 (#14643) + - add missing PCRE dependency for pullseq + add sanity check commands (#14650) + - use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs (#14655) + - fix name for (binary) AutoDock-Vina v1.1.2 (#14675) + - add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (#14726) + - set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with: + - TensorFlow 2.2.3-2.4.1 with 2020* toolchain (#14729) and 2.5.0+ (#14728) + - Ray-project (#14730) + - update build dependencies for binutils 2.37 with system toolchain (#14731) + - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) + - enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (#14741) + - add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (#14743) + - also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (#14745) + - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14755) + - do not use external libgcrypt or python for libxslt with recent toolchains (#14756) + - fix CVE-2021-23437 in: + - Pillow v7 and v8 + update to Pillow v8.3.2 in easyconfigs using a 2021b toolchain (#14765) + - Pillow-SIMD v7 and v8 + add easyconfig for Pillow-SIMD v8.3.2 with GCCcore/11.2.0 (#14792) + - only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths (#14769) + - add libXfont2 patch to fix build when libbsd is present (#14821) +- other changes: + - update Java 1.8 wrapper to 1.8.0_311 for x86_64 (#14644) + - bring gffread back down to GCCcore level for toolchain version 10.3.0 (#14660) + - stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 (#14734) + + v4.5.1 (December 13th 2021) --------------------------- diff --git a/setup.py b/setup.py index bb5b73a292d..663b9046087 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.2.dev0' +VERSION = '4.5.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From de2a8651cc567d53e6f0d2c0f979cb55f44a7755 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Jan 2022 17:11:07 +0100 Subject: [PATCH 528/528] minor tweak release notes for v4.5.2 --- RELEASE_NOTES | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 24bac8fac8f..79e2add3b6c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 13,812 easyconfig files, for 2,575 different software packages, +The latest version of easybuild-easyconfig provides 14,080 easyconfig files, for 2,622 different software packages, incl. 36 different (compiler) toolchains. @@ -12,6 +12,7 @@ v4.5.2 (January 24th 2022) update/bugfix release +- added easyconfig for intel/2022.00 toolchain (#14620) - added example easyconfig files for 48 new software packages: - alevin-fry (#14617), AMD-uProf (#14626), ANGEL (#11857), atropos (#7580), Austin (#14596), AutoDock-GPU (#14671), AutoDock-Vina (#14675), boost_histogram (#14516), CAFE5 (#14603), Calcam (#7488), Carma (#14527), Cogent (#14278), @@ -20,21 +21,26 @@ update/bugfix release IsoNet (#14075), MACSE (#14709), MetaPhlAn (#12917), MicrobeAnnotator (#14549), mold (#14595), numdiff (#14609), OpenFace (#14556), PhyloPhlAn (#14564), PREQUAL (#14722), PuLP (#14581), PyCalib (#14616), PyTorch3D (#13240), QCG-PilotJob (#14337), RaGOO (#8995), RAPSearch2 (#13199), SCopeLoomR (#14518), ShengBTE (#14557), SHTns (#14682), - STRUMPACK (#14560), TALYS (#14716), TN93 xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) + STRUMPACK (#14560), TALYS (#14716), TN93 (#14691), xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) - added additional easyconfigs for various supported software packages, including: - - AdapterRemoval 2.3.2, alevin fry, AMD uProf, AMOS 3.1.0, Anaconda3 2021.11.eb, ANGEL 3.0, annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, arpack ng, Arrow 0.17.1, Arrow 6.0.1, atropos 1.1.21, Austin 3.2.0, Austin 3.2.0.eb, AutoDock 4.2.6, AutoDock GPU, AutoDock Vina, AutoDock Vina, Bazel 3.7.2, bcl2fastq2 2.20.0, Bismark 0.23.1, Bison 3.8.2.eb, BLAST+ 2.12.0, Blender 3.0.0, boost_histogram 1.2.1, Bowtie2 2.4.4, BWA 0.7.17, CAFE5 5.0.0, Calcam 2.1.0, Calcam 2.1.0, canu 2.2, Carma 2.01, CD HIT, cDNA_Cupcake 24.2.0, cDNA_Cupcake 26.0.0, CDO 1.9.10, CGAL 4.14.3, CheckM 1.1.3, CHERAB 1.3.0, CHERAB 1.3.0, CMake 3.20.1, CMake 3.22.1, Cogent 8.0.0, CompareM 0.1.2, CP2K 8.2, CUDAcore 11.4.0.eb, CVXOPT 1.2.3, Cython 3.0a5, DAS_Tool 1.1.1, DendroPy 4.5.2, DIAMOND 2.0.13, DIAMOND 2.0.13, dill 0.3.4, dlib 19.22, dlib 19.22, dotNET Core, dotNET SDK, DualSPHysics 5.0.175, DualSPHysics 5.0.175, dune core, dune fem, DyMat 0.7, EasyBuild 4.5.1.eb, Eigen 3.4.0, EIGENSOFT 7.2.1, elbencho 2.0, ELSI RCI, ELSI RCI, ELSI RCI, ELSI RCI, Embree 3.4.0, ExaML 3.0.22, expecttest 0.1.3, Extrae 3.8.3, fastp 0.23.2, FastTree 2.1.11, FMPy 0.3.2, FragGeneScan 1.31, FreeImage 3.18.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FTGL 2.1.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, gengetopt 2.23, genozip 13.0.5, georges 2019.2, GffCompare 0.12.6, gffread 0.12.7, gffread 0.12.7, gmsh 4.9.0, gnuplot 5.4.2, graphite2 1.3.14, GSL 2.7, GTDB Tk, GTK3 3.24.31, h5py 3.6.0, h5py 3.6.0, hivtrace 0.6.2, HMMER 3.3.2, Horovod 0.23.0, HPL 2.3, hypothesis 4.57.1, IDBA UD, igraph 0.9.5, iimpi 2022.00.eb, imkl 2022.0.1.eb, imkl FFTW, impi 2021.5.0, Inspector 2022.0.0.eb, intel 2022.00.eb, intel compilers, intervaltree python, IPython 5.10.0, IQ TREE, ISA L, IsoNet 0.1_20210822_04_674f67f, itac 2021.2.0.eb, itac 2021.5.0.eb, Java 15.0.1.eb, Java 15.eb, Java 17.0.1.eb, Java 17.eb, Java 1.8.0_311.eb, JUBE 2.4.2.eb, Julia 1.6.5, Julia 1.7.1, Kaleido 0.2.1, KronaTools 2.8.1, leidenalg 0.8.8, libdeflate 1.8, libdwarf 20210305, libelf 0.8.13, libgd 2.3.3, Libint 2.6.0, libxsmm 1.17, LMfit 1.0.3, LSD2 2.3, MACSE 2.06, MAGMA 1.09b, mapDamage 2.2.1, MATLAB 2021b.eb, matplotlib 2.2.5, MaxBin 2.2.7, MEGAHIT 1.2.9, MetaBAT 2.15, MetaPhlAn 3.0.9, MicrobeAnnotator 2.0.5, MinPath 1.6, mold 0.9.6, mold 1.0.0, molmod 1.4.8, MultiQC 1.10.1, MultiQC 1.11, MUMmer 4.0.0beta2, MUSCLE 3.8.31, MUSCLE 3.8.31, MUSCLE 5.0.1428, ncview 2.1.8, NGS Python, numba 0.50.1, numba 0.54.1, numdiff 5.9.0, NVHPC 21.11.eb, OBITools 1.2.13, occt 7.5.0p1, OpenBabel 3.1.1, openCARP 8.2, OpenCV 3.4.1, OpenFace 2.2.0, OpenFace 2.2.0, OpenFOAM v2112, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, PAML 4.9j, parasail 2.4.3, ParaView 5.9.1, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, PEAR 0.9.11, phonopy 2.12.0, PhyloPhlAn 3.0, PhyloPhlAn 3.0.2, Pillow 8.3.2, Pillow SIMD, plotly.py 4.14.3, PLUMED 2.7.2, PLUMED 2.7.3, poppler 22.01.0, PREQUAL 1.02, PRINSEQ 0.20.4, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, pullseq 1.0.2, PuLP 2.5.1, pybind11 2.7.1, PyCairo 1.20.1, PyCalib 0.1.0.dev0, PyOpenCL 2021.1.2, PyOpenGL 3.1.5, PyQt5 5.9.2, PyQtGraph 0.12.3, Python 2.7.18, python igraph, python parasail, PyTorch 1.10.0, PyTorch3D 0.4.0, PyZMQ 22.3.0, QCG PilotJob, Qt5 5.15.2, RaGOO 1.11, RAPSearch2 2.24, RAxML 8.2.12, Raysect 0.7.1, Raysect 0.7.1, RDP Classifier, Rgurobi 9.5.0, Ruby 3.0.1, scanpy 1.8.2, Schrodinger 2021, SciPy bundle, SCopeLoomR 0.13.0, SCOTCH 6.1.2, SEPP 4.3.10, SEPP 4.5.0, SEPP 4.5.1, seqtk 1.3, ShengBTE 1.1.1, Short Pair, SHTns 2.7, SHTns 3.5.1, SIP 4.19.8, Spack 0.17.0.eb, SPAdes 3.15.3, Spark 3.1.1, SqueezeMeta 1.0.0, STAR 2.7.9a, statsmodels 0.13.1, statsmodels 0.13.1, STRUMPACK 6.1.0, STRUMPACK 6.1.0, Subread 2.0.3, SuiteSparse 5.10.1, TALYS 1.95, TALYS 1.95, texlive 20210324, Tkinter 2.7.18, TN93 1.0.7, TreeMix 1.13, trimAl 1.4.1, VCFtools 0.1.16, VTune 2022.0.0.eb, worker 1.6.12, wtdbg2 2.5, XML LibXML, xxHash 0.8.0, yaff 1.6.0, yaml cpp, Zgoubi 6.0.2 + - annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0, + cDNA_Cupcake 26.0.0, CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, dotNET-Core-Runtime 6.0.1, + dotNET-SDK 6.0.101, Extrae 3.8.3, fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, GTK3 3.24.31, + h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2, + libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428, + numba 0.54.1, NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 3.4.1, OpenFOAM v2112, ORCA 5.0.2, + phonopy 2.12.0, Pillow 8.3.2, Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 0.12.3, + python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 1.0.0, + statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0 - minor enhancements, including: - add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (#14547) - include output of failing code style check in message produced by failing easyconfigs style test (#14578) - - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591) - - add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig (#14634) - - add FactorCopula extension for R v4.1.2 (#14648) - - add ExomeDepth extension to R-bundle-Bioconductor 3.14 (#14684) - - add DSS extension to R-bundle-Bioconductor 3.14 (#14748) - - add rpact and ldbounds extensions to R v4.1.2 (#14750) - - add pathview extension to R-bundle-Bioconductor 3.14 (#14806) + - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591, #14769) + - add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX (#14634), FactorCopula (#14648), rpact, ldbounds (#14750) + - add extensions to R-bundle-Bioconductor 3.14: ExomeDepth (#14684), DSS (#14748), pathview (#14806) - various bug fixes, including: - fix homepage and source_urls for GLIMMER 3.02b (#7945) + - fix source URL for Trilinos 12.12.1 with foss/2019b (#14547) - use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (#14565) - fix checksum and versions of annovar v20191024 (#14579) - add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (#14584) @@ -50,22 +56,17 @@ update/bugfix release - set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with: - TensorFlow 2.2.3-2.4.1 with 2020* toolchain (#14729) and 2.5.0+ (#14728) - Ray-project (#14730) - - update build dependencies for binutils 2.37 with system toolchain (#14731) - - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) - enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (#14741) - add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (#14743) - also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (#14745) - - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14755) - do not use external libgcrypt or python for libxslt with recent toolchains (#14756) - - fix CVE-2021-23437 in: - - Pillow v7 and v8 + update to Pillow v8.3.2 in easyconfigs using a 2021b toolchain (#14765) - - Pillow-SIMD v7 and v8 + add easyconfig for Pillow-SIMD v8.3.2 with GCCcore/11.2.0 (#14792) - - only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths (#14769) + - add patches to fix CVE-2021-23437 for Pillow (#14765) and Pillow-SIMD (#14792) - add libXfont2 patch to fix build when libbsd is present (#14821) - other changes: - update Java 1.8 wrapper to 1.8.0_311 for x86_64 (#14644) - bring gffread back down to GCCcore level for toolchain version 10.3.0 (#14660) - - stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 (#14734) + - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14731, #14755) + - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) v4.5.1 (December 13th 2021)