From 9852fe7458a6ee97fa5580d15015b9af03fb8a01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 11 Oct 2024 16:16:27 +0200 Subject: [PATCH 1/3] adding easyconfigs: Cellformer-20240917-foss-2023a-R-4.3.2.eb --- .../Cellformer-20240917-foss-2023a-R-4.3.2.eb | 188 ++++++++++++++++++ 1 file changed, 188 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..4f21285268a --- /dev/null +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -0,0 +1,188 @@ +easyblock = 'Tarball' + +name = 'Cellformer' +version = '20240917' +versionsuffix = '-R-%(rver)s' +local_commit = '99a1165' + +homepage = 'https://github.com/elo-nsrb/Cellformer' +description = '''An implementation of Cellformer from our publication: Berson et al. + "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature"''' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/elo-nsrb/Cellformer/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['7cbddad75a4d47dfc0a39cd660ef20fe4e3cb755631b1b96136c1c3d5226c914'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), + ('scikit-learn', '1.3.1'), + ('PyTorch-Lightning', '2.2.1'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('SciPy-bundle', '2023.07'), + ('Seaborn', '0.13.2'), + ('tensorboard', '2.15.1'), + ('tensorboardX', '2.6.2.2'), + ('torchvision', '0.16.0'), + ('tqdm', '4.66.1'), + ('scanpy', '1.9.8'), + ('pretty-yaml', '24.7.0'), + ('Arrow', '14.0.1'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('ArchR', '1.0.2', versionsuffix), + ('typing-extensions', '4.9.0'), + ('einops', '0.7.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('typing_extensions', '4.12.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d'], + }), + ('asteroid_filterbanks', '0.4.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4932ac8b6acc6e08fb87cbe8ece84215b5a74eee284fe83acf3540a72a02eaf5'], + }), + ('huggingface_hub', '0.25.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1897caf88ce7f97fe0110603d8f66ac264e3ba6accdf30cd66cc0fed5282ad25'], + }), + ('julius', '0.2.7', { + 'checksums': ['3c0f5f5306d7d6016fcc95196b274cae6f07e2c9596eed314e4e7641554fbb08'], + }), + ('cached_property', '1.5.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0'], + }), + ('mir_eval', '0.7', { + 'checksums': ['e1febaa5766c65a7545c2a170b241490f47a98987370b1e06742424c5debe65e'], + }), + ('pesq', '0.0.4', { + 'checksums': ['b724b28f73fb638522982bd68e8c3c0957e2f45210639a460233b17aa7fc890b'], + }), + ('pb_bss_eval', '0.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a72c2fd04c9f4a4e734cf615029c3877e6e4536225eeaaae05bb0cf014b3af1b'], + }), + ('soundfile', '0.12.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['828a79c2e75abab5359f780c81dccd4953c45a2c4cd4f05ba3e233ddf984b882'], + }), + ('pytorch_ranger', '0.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1e69156c9cc8439185cb8ba4725b18c91947fbe72743e25aca937da8aeb0c8ec'], + }), + ('torch_optimizer', '0.1.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['b7adaed38b66a5c5105a59b30a71c4ab7c9954baf0acabd969fee3dac954657d'], + }), + ('pystoi', '0.4.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['e277b671663d26d35a2416c9c8010a74084e6c3970354506398051a554896939'], + }), + ('torch_stoi', '0.2.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6eee85e33b42fe843a2150de46000f72e7b87cbeb19ae6ab9bbd94b6ec6b3cd2'], + }), + ('torchmetrics', '1.4.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['76e67490231acef7f70cf36ab129df72fb2b0256dada7051001ab3b9f8699bf4'], + }), + ('asteroid', '0.7.0', { + 'checksums': ['0326f28c5342495cb08ba0520efd0e21e39435dfd78854837fdd5a6c9c9ca410'], + }), + ('everett', '3.1.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['db13891b849e45e54faea93ee79881d12458c5378f5b9b7f806eeff03ce1de3c'], + }), + ('configobj', '5.0.9', { + 'checksums': ['03c881bbf23aa07bccf1b837005975993c4ab4427ba57f959afdd9d1a2386848'], + }), + ('python_box', '6.1.0', { + 'modulename': 'box', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['bdec0a5f5a17b01fc538d292602a077aa8c641fb121e1900dff0591791af80e8'], + }), + ('sentry_sdk', '2.15.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8fb0d1a4e1a640172f31502e4503543765a1fe8a9209779134a4ac52d4677303'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('comet_ml', '3.47.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['81062bbef2d0758c8e77d8a469824d2c20ec13b09855c78b51b078203628b8c2'], + }), + ('fast_histogram', '0.14', { + 'checksums': ['390973b98af22bda85c29dcf6f008ba0d626321e9bd3f5a9d7a43e5690ea69ea'], + }), + ('mpl_scatter_density', '0.7', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['721b4efeafcbc0ba4a5c1ecd8f401dc2d1aa6a372445c5b49e1da34e70a95ead'], + }), + ('tensorboard_data_server', '0.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['753d4214799b31da7b6d93837959abebbc6afa86e69eacf1e9a317a48daa31eb'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('torchmetrics', '1.4.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87b9eca51ff6f93985a0f9db509f646cb45425b016f4d2f383d8c28d40dde5b6'], + }), + ('torchmetrics', '0.11.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['45f892f3534e91f3ad9e2488d1b05a93b7cb76b7d037969435a41a1f24750d9a'], + }), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +fix_python_shebang_for = [ + 'src/*/*.py', + 'src/*/*/*.py', + 'src/*/*/*/*.py', +] + +local_scripts = [ + 'createPeakMatrix.sh', + 'createDataset.sh', + 'deconvolution.sh', + 'trainModel.sh', + 'validation.sh', +] + +postinstallcmds = [ + "sed -i 's|python |python %(installdir)s/|g' %(installdir)s/*.sh" +] + ['chmod a+rx %%(installdir)s/%s' % script for script in local_scripts] + +sanity_check_paths = { + 'files': local_scripts, + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%s --help | grep '^Usage:'" % script for script in local_scripts] + +moduleclass = 'bio' From 5ac6d9b8705b95306e25b7e954cf155be5b40699 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 11 Oct 2024 18:42:23 +0200 Subject: [PATCH 2/3] patch requirements --- .../c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb index 4f21285268a..229fbc757ee 100644 --- a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -104,6 +104,8 @@ exts_list = [ 'checksums': ['76e67490231acef7f70cf36ab129df72fb2b0256dada7051001ab3b9f8699bf4'], }), ('asteroid', '0.7.0', { + # requirement too strict + 'preinstallopts': "sed -i 's/torchmetrics<=0.11.4/torchmetrics/g' setup.py && ", 'checksums': ['0326f28c5342495cb08ba0520efd0e21e39435dfd78854837fdd5a6c9c9ca410'], }), ('everett', '3.1.0', { From 2b1f38528066a617e51288929be3669399f685e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 16 Oct 2024 12:19:35 +0200 Subject: [PATCH 3/3] remove `typing-extensions` from `exts_list` --- .../c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb index 229fbc757ee..67df72c221f 100644 --- a/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb @@ -50,10 +50,6 @@ exts_default_options = { } exts_list = [ - ('typing_extensions', '4.12.2', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d'], - }), ('asteroid_filterbanks', '0.4.0', { 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['4932ac8b6acc6e08fb87cbe8ece84215b5a74eee284fe83acf3540a72a02eaf5'],