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Merge pull request #10938 from easybuilders/4.2.x
release EasyBuild v4.2.2
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85 changes: 85 additions & 0 deletions
85
easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb
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| ## | ||
| # This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia | ||
| # Homepage: https://staff.flinders.edu.au/research/deep-thought | ||
| # | ||
| # Authors:: Robert Qiao <[email protected]> | ||
| # Software License:: MIT | ||
| # | ||
| # Notes:: | ||
| ## | ||
|
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| easyblock = 'CmdCp' | ||
|
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| name = 'AmrPlusPlus' | ||
| version = '2.0-20200114' | ||
| local_commit = '8afc0af5234f8e322cc0f5e40cc553ecd5c932b8' | ||
|
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| github_account = 'meglab-metagenomics' | ||
|
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| homepage = 'https://megares.meglab.org/amrplusplus/latest/html/v2' | ||
| description = """AmrPlusPlus v2.0 can process the raw data from the sequencer, | ||
| identify the fragments of DNA, and count them. It also provides a count of the | ||
| polymorphisms that occur in each DNA fragment with respect to the reference database. | ||
| """ | ||
|
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| toolchain = {'name': 'GCC', 'version': '8.3.0'} | ||
|
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| source_urls = ['https://github.com/%(github_account)s/%(name)s_v%(version_major)s/archive'] | ||
| sources = [{ | ||
| 'download_filename': '%s.zip' % local_commit, | ||
| 'filename': SOURCE_ZIP, | ||
| }] | ||
| checksums = ['04af67517b752e15b5add27f4584f8c11293a0ed1353d3c1dd60c3c6e2dcb329'] | ||
|
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| dependencies = [ | ||
| ('Java', '11', '', True), | ||
| ('BWA', '0.7.17'), | ||
| ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), | ||
| ('SAMtools', '1.10'), | ||
| ('Nextflow', '19.12.0', '', True), | ||
| ] | ||
|
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| local_exe_files = [ | ||
| 'main_AmrPlusPlus_v2.nf', | ||
| 'main_AmrPlusPlus_v2_withKraken.nf', | ||
| 'main_AmrPlusPlus_v2_withRGI_Kraken.nf', | ||
| 'main_AmrPlusPlus_v2_withRGI.nf', | ||
| 'launch_mpi_slurm.sh', | ||
| 'download_minikraken.sh', | ||
| 'nextflow.config' | ||
| ] | ||
|
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| local_dir = ['bin', 'data', 'docs', 'config'] | ||
|
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| local_files = [ | ||
| 'main_AmrPlusPlus_v2.nf', | ||
| 'bin/RGI_aro_hits.py', | ||
| 'bin/RGI_long_combine.py', | ||
| 'bin/samtools_idxstats.py', | ||
| 'bin/kraken_long_to_wide.py', | ||
| 'bin/trimmomatic_stats.py' | ||
| ] | ||
|
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| skipsteps = ['configure', 'build'] | ||
|
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| files_to_copy = [ | ||
| (local_exe_files, '%(installdir)s'), | ||
| (local_dir, '%(installdir)s') | ||
| ] | ||
|
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| install_cmd = "chmod +x %(installdir)s/*.nf && " | ||
| install_cmd += "chmod +x %(installdir)s/*.sh" | ||
|
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| modextravars = { | ||
| 'JAVA': '${EBROOTJAVA}/bin/java', | ||
| 'BWA': '${EBROOTBWA}/bin/bwa' | ||
| } | ||
|
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| modloadmsg = """To execute AmrPlusPlus, run:\n nextflow run $EBROOTAMRPLUSPLUS/main_AmrPlusPlus_v2.nf [options]\n""" | ||
|
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| sanity_check_paths = { | ||
| 'files': ['%s' % x for x in local_files], | ||
| 'dirs': ['config'] | ||
| } | ||
|
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| moduleclass = 'bio' |
28 changes: 28 additions & 0 deletions
28
easybuild/easyconfigs/a/Armadillo/Armadillo-9.600.5-foss-2018b.eb
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|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| name = 'Armadillo' | ||
| version = '9.600.5' | ||
|
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| homepage = 'https://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.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2018b'} | ||
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| source_urls = ['https://sourceforge.net/projects/arma/files'] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| patches = [ | ||
| 'Armadillo-9.600.5_no_mkl.patch', | ||
| ] | ||
| checksums = [ | ||
| 'dd9cd664282f2c3483af194ceedc2fba8559e0d20f8782c640fd6f3ac7cac2bf', # source | ||
| '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch | ||
| ] | ||
|
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| dependencies = [ | ||
| ('Boost', '1.67.0'), | ||
| ('arpack-ng', '3.5.0'), | ||
| ] | ||
|
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| builddependencies = [('CMake', '3.12.1')] | ||
|
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| moduleclass = 'numlib' |
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11
easybuild/easyconfigs/a/Armadillo/Armadillo-9.600.5_no_mkl.patch
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| --- CMakeLists.txt.orig 2016-06-16 18:20:05.000000000 +0200 | ||
| +++ CMakeLists.txt 2019-10-22 10:44:59.764711121 +0200 | ||
| @@ -173,7 +173,7 @@ | ||
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| set(ARMA_OS unix) | ||
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| - include(ARMA_FindMKL) | ||
| + set(MKL_FOUND false) | ||
| include(ARMA_FindACMLMP) | ||
| include(ARMA_FindACML) | ||
| include(ARMA_FindOpenBLAS) |
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28 changes: 28 additions & 0 deletions
28
easybuild/easyconfigs/a/Armadillo/Armadillo-9.880.1-foss-2020a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| name = 'Armadillo' | ||
| version = "9.880.1" | ||
|
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| homepage = 'https://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.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2020a'} | ||
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| source_urls = ['https://sourceforge.net/projects/arma/files'] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| patches = [ | ||
| 'Armadillo-9.600.5_no_mkl.patch', | ||
| ] | ||
| checksums = [ | ||
| '900f3e8d35d8b722217bed979fa618faf6f3e4f56964c887a1fce44c3d4c4b9f', # src | ||
| '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch | ||
| ] | ||
|
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| dependencies = [ | ||
| ('Boost', '1.72.0'), | ||
| ('arpack-ng', '3.7.0'), | ||
| ] | ||
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| builddependencies = [('CMake', '3.16.4')] | ||
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| moduleclass = 'numlib' |
28 changes: 28 additions & 0 deletions
28
easybuild/easyconfigs/a/Armadillo/Armadillo-9.900.1-foss-2019b.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| name = 'Armadillo' | ||
| version = "9.900.1" | ||
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| homepage = 'https://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.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2019b'} | ||
|
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| source_urls = ['https://sourceforge.net/projects/arma/files'] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| patches = [ | ||
| 'Armadillo-9.600.5_no_mkl.patch' | ||
| ] | ||
| checksums = [ | ||
| '53d7ad6124d06fdede8d839c091c649c794dae204666f1be0d30d7931737d635', # src | ||
| '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch | ||
| ] | ||
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| dependencies = [ | ||
| ('Boost', '1.71.0'), | ||
| ('arpack-ng', '3.7.0'), | ||
| ] | ||
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| builddependencies = [('CMake', '3.15.3')] | ||
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| moduleclass = 'numlib' |
28 changes: 28 additions & 0 deletions
28
easybuild/easyconfigs/a/Armadillo/Armadillo-9.900.1-foss-2020a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| name = 'Armadillo' | ||
| version = "9.900.1" | ||
|
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| homepage = 'https://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.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2020a'} | ||
|
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| source_urls = ['https://sourceforge.net/projects/arma/files'] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| patches = [ | ||
| 'Armadillo-9.600.5_no_mkl.patch' | ||
| ] | ||
| checksums = [ | ||
| '53d7ad6124d06fdede8d839c091c649c794dae204666f1be0d30d7931737d635', # src | ||
| '8288e769ceaf06da9f6870f616272c354577b1dd6f07e923fed43b22bae131b6', # Armadillo-9.600.5_no_mkl.patch | ||
| ] | ||
|
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| dependencies = [ | ||
| ('Boost', '1.72.0'), | ||
| ('arpack-ng', '3.7.0'), | ||
| ] | ||
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| builddependencies = [('CMake', '3.16.4')] | ||
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| moduleclass = 'numlib' |
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67
easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| easyblock = 'CMakeMake' | ||
|
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| name = 'Arrow' | ||
| version = '0.17.1' | ||
| versionsuffix = '-Python-%(pyver)s' | ||
|
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| homepage = 'https://arrow.apache.org' | ||
| description = """Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform | ||
| for in-memory data.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2020a'} | ||
|
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| 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 | ||
| ] | ||
|
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| builddependencies = [ | ||
| ('CMake', '3.16.4'), | ||
| ('Autotools', '20180311'), | ||
| ('flex', '2.6.4'), | ||
| ('Bison', '3.5.3'), | ||
| ('pkg-config', '0.29.2'), | ||
| ] | ||
|
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| # Arrow strongly prefers included jemalloc, so not including it as a dependency | ||
| dependencies = [ | ||
| ('Python', '3.8.2'), | ||
| ('SciPy-bundle', '2020.03', versionsuffix), # for numpy | ||
| ('Boost', '1.72.0'), | ||
| ] | ||
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| separate_build_dir = True | ||
| start_dir = 'cpp' | ||
|
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| # 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" | ||
|
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| # 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] | ||
|
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| modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} | ||
|
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| 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'], | ||
| } | ||
|
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| sanity_check_commands = [ | ||
| "python -c 'import pyarrow'", | ||
| "python -c 'import pyarrow.parquet'", | ||
| ] | ||
|
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| moduleclass = 'data' |
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