{bio}[foss/2023a] DeepLoc v2.0, ONNX-Runtime v1.19.2, ESM-2 v2.0.0

easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb

@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'DeepLoc'
+version = '2.0'
+
+homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0'
+description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('Biopython', '1.83'),
+    ('ONNX-Runtime', '1.19.2'),
+    ('ESM-2', '2.0.0'),  # for fair-esm
+    ('PyTorch', '2.1.2'),
+    ('PyTorch-Lightning', '2.2.1'),
+    ('Transformers', '4.39.3'),
+    ('SentencePiece', '0.2.0'),
+    ('mygene', '3.2.2'),  # required by bio
+]
+
+use_pip = True
+
+local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?'
+local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All'
+
+exts_list = [
+    ('gprofiler-official', '1.0.0', {
+        'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'],
+        'modulename': 'gprofiler',
+    }),
+    ('bio', '1.7.1', {
+        'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'],
+        'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'],
+        'modulename': 'biorun',
+    }),
+    (name, version, {
+        'download_instructions': "Download via %s" % local_deeploc_download_url,
+        'sources': ['deeploc-%(version)s.All.tar.gz'],
+        'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'],
+        'modulename': 'DeepLoc2',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/deeploc2'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "deeploc2 --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb

@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'ESM-2'
+version = '2.0.0'
+
+homepage = 'https://github.com/facebookresearch/esm'
+description = """ESM-2 outperforms all tested single-sequence protein language models
+ across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate
+ accurate structure predictions end to end directly from the sequence of a protein."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Java', '11', '', SYSTEM),  # needed by ANTLR4 runtime
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# omegaconf is required for esmfold (in addition to OpenFold-1.0.1)
+exts_list = [
+    ('antlr4-python3-runtime', '4.9.3', {
+        'modulename': 'antlr4',
+        'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'],
+    }),
+    ('omegaconf', '2.3.0', {
+        'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'],
+    }),
+    ('fair-esm', version, {
+        'modulename': "esm, esm.pretrained",
+        'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb

@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'ONNX-Runtime'
+version = '1.19.2'
+
+homepage = 'https://onnxruntime.ai'
+description = """ONNX Runtime inference can enable faster customer experiences and lower costs,
+supporting models from deep learning frameworks such as PyTorch and
+TensorFlow/Keras as well as classical machine learning libraries such as
+scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different
+hardware, drivers, and operating systems, and provides optimal performance by
+leveraging hardware accelerators where applicable alongside graph optimizations
+and transforms."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('ONNX', '1.15.0'),
+    ('flatbuffers-python', '23.5.26'),
+    ('sympy', '1.12'),
+]
+
+use_pip = True
+
+local_whl_tmpl = 'onnxruntime-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl'
+
+exts_list = [
+    ('humanfriendly', '10.0', {
+        'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
+    }),
+    ('coloredlogs', '15.0.1', {
+        'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
+    }),
+    (name, version, {
+        'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime'],
+        'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')],
+        'checksums': [{
+            local_whl_tmpl % ('x86_64', 'x86_64'):
+                'a36511dc07c5c964b916697e42e366fa43c48cdb3d3503578d78cef30417cb84',
+            local_whl_tmpl % ('aarch64', 'aarch64'):
+                'c1dfe4f660a71b31caa81fc298a25f9612815215a47b286236e61d540350d7b6',
+        }],
+        'modulename': 'onnxruntime',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'devel'