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Merge pull request #20551 from pavelToman/20240517134249_new_pr_CellB…
…ender030 {tools}[foss/2023a] CellBender v0.3.0, jupyter-contrib-nbextensions v0.7.0, pyro-ppl v1.9.0
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72 changes: 72 additions & 0 deletions
72
easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb
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easyblock = 'PythonBundle' | ||
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name = 'CellBender' | ||
version = '0.3.0' | ||
versionsuffix = '-CUDA-%(cudaver)s' | ||
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homepage = 'http://github.com/broadinstitute/CellBender' | ||
description = """ | ||
CellBender is a software package for eliminating technical artifacts from | ||
high-throughput single-cell RNA sequencing (scRNA-seq) data. | ||
""" | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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dependencies = [ | ||
('CUDA', '12.1.1', '', SYSTEM), | ||
('Python', '3.11.3'), | ||
('SciPy-bundle', '2023.07'), | ||
('matplotlib', '3.7.2'), | ||
('PyTorch', '2.1.2', versionsuffix), | ||
('IPython', '8.14.0'), | ||
('anndata', '0.10.5.post1'), | ||
('jupyter-contrib-nbextensions', '0.7.0'), | ||
('pyro-ppl', '1.9.0', versionsuffix), | ||
('loompy', '3.0.7'), | ||
('PyTables', '3.8.0'), | ||
('Qtconsole', '5.5.1'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('async-timeout', '4.0.3', { | ||
'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], | ||
}), | ||
('traitlets', '5.14.1', { | ||
'source_tmpl': SOURCE_PY3_WHL, | ||
'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], | ||
}), | ||
('jupyter_console', '6.6.3', { | ||
'source_tmpl': SOURCE_PY3_WHL, | ||
'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], | ||
}), | ||
('jupyter', '1.0.0', { | ||
'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], | ||
}), | ||
('notebook', '6.5.7', { | ||
'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], | ||
}), | ||
('mistune', '0.8.4', { | ||
'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], | ||
}), | ||
('nbconvert', '6.5.4', { | ||
'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'], | ||
}), | ||
('cellbender', version, { | ||
'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'], | ||
}), | ||
] | ||
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sanity_check_paths = { | ||
'files': ['bin/cellbender'], | ||
'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
} | ||
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sanity_check_commands = [ | ||
"cellbender --help", | ||
] | ||
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sanity_pip_check = True | ||
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moduleclass = 'bio' |
70 changes: 70 additions & 0 deletions
70
easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb
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easyblock = 'PythonBundle' | ||
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name = 'CellBender' | ||
version = '0.3.0' | ||
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homepage = 'http://github.com/broadinstitute/CellBender' | ||
description = """ | ||
CellBender is a software package for eliminating technical artifacts from | ||
high-throughput single-cell RNA sequencing (scRNA-seq) data. | ||
""" | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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dependencies = [ | ||
('Python', '3.11.3'), | ||
('SciPy-bundle', '2023.07'), | ||
('matplotlib', '3.7.2'), | ||
('PyTorch', '2.1.2'), | ||
('IPython', '8.14.0'), | ||
('anndata', '0.10.5.post1'), | ||
('jupyter-contrib-nbextensions', '0.7.0'), | ||
('pyro-ppl', '1.9.0'), | ||
('loompy', '3.0.7'), | ||
('PyTables', '3.8.0'), | ||
('Qtconsole', '5.5.1'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('async-timeout', '4.0.3', { | ||
'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], | ||
}), | ||
('traitlets', '5.14.1', { | ||
'source_tmpl': SOURCE_PY3_WHL, | ||
'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], | ||
}), | ||
('jupyter_console', '6.6.3', { | ||
'source_tmpl': SOURCE_PY3_WHL, | ||
'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], | ||
}), | ||
('jupyter', '1.0.0', { | ||
'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], | ||
}), | ||
('notebook', '6.5.7', { | ||
'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], | ||
}), | ||
('mistune', '0.8.4', { | ||
'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], | ||
}), | ||
('nbconvert', '6.5.4', { | ||
'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'], | ||
}), | ||
('cellbender', version, { | ||
'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'], | ||
}), | ||
] | ||
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sanity_check_paths = { | ||
'files': ['bin/cellbender'], | ||
'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
} | ||
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sanity_check_commands = [ | ||
"cellbender --help", | ||
] | ||
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sanity_pip_check = True | ||
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moduleclass = 'bio' |
62 changes: 62 additions & 0 deletions
62
...nfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb
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easyblock = "PythonBundle" | ||
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name = 'jupyter-contrib-nbextensions' | ||
version = '0.7.0' | ||
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homepage = 'https://github.com/ipython-contrib/jupyter_contrib_nbextensions' | ||
description = 'A collection of various notebook extensions for Jupyter' | ||
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toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
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builddependencies = [ | ||
('binutils', '2.40'), | ||
('nodejs', '18.17.1'), | ||
] | ||
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dependencies = [ | ||
('Python', '3.11.3'), | ||
('IPython', '8.14.0'), | ||
('PyYAML', '6.0'), | ||
('jupyter-server', '2.7.2'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('entrypoints', '0.4', { | ||
'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], | ||
}), | ||
('nbclassic', '1.0.0', { | ||
'checksums': ['0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'], | ||
}), | ||
# need jupyter_client in v7 - notebook 6.5.7 has requirement jupyter-client<8,>=5.3.4 | ||
('jupyter_client', '7.4.9', { | ||
'checksums': ['52be28e04171f07aed8f20e1616a5a552ab9fee9cbbe6c1896ae170c3880d392'], | ||
}), | ||
# use notebook v6, in v7 the extension are moved to jupyter lab | ||
('notebook', '6.5.7', { | ||
'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'], | ||
}), | ||
('jupyter_contrib_core', '0.4.2', { | ||
'checksums': ['1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb'], | ||
}), | ||
('jupyter_highlight_selected_word', '0.2.0', { | ||
'checksums': ['9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b'], | ||
}), | ||
('jupyter_nbextensions_configurator', '0.6.3', { | ||
'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', | ||
'checksums': ['cece496f3f62cf80bb0b04867ea463c32ed5db19ff5814fe18a3a7f1bb9da95b'], | ||
}), | ||
('jupyter_contrib_nbextensions', version, { | ||
'checksums': ['06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca'], | ||
}), | ||
] | ||
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sanity_pip_check = True | ||
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sanity_check_paths = { | ||
'files': ['bin/jupyter-contrib', 'bin/jupyter-contrib-nbextension', 'bin/jupyter-nbextensions_configurator'], | ||
'dirs': ['lib64/python%(pyshortver)s/site-packages'] | ||
} | ||
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moduleclass = 'tools' |
47 changes: 47 additions & 0 deletions
47
easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb
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# Author: Denis Krišťák (INUITS) | ||
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easyblock = 'PythonBundle' | ||
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name = 'pyro-ppl' | ||
version = '1.9.0' | ||
versionsuffix = '-CUDA-%(cudaver)s' | ||
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homepage = 'https://github.com/pyro-ppl/pyro' | ||
description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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dependencies = [ | ||
('CUDA', '12.1.1', '', SYSTEM), | ||
('Python', '3.11.3'), | ||
('SciPy-bundle', '2023.07'), | ||
('PyTorch', '2.1.2', versionsuffix), | ||
('tqdm', '4.66.1'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('opt-einsum', '3.3.0', { | ||
'source_tmpl': 'opt_einsum-%(version)s.tar.gz', | ||
'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], | ||
}), | ||
('pyro-api', '0.1.2', { | ||
'modulename': 'pyroapi', | ||
'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], | ||
}), | ||
(name, version, { | ||
'modulename': 'pyro', | ||
'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'], | ||
}), | ||
] | ||
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sanity_pip_check = True | ||
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sanity_check_commands = [ | ||
"python -c 'from pyroapi import distributions as dist'", | ||
"python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", | ||
"python -c 'from pyro import infer, nn, distributions'", | ||
] | ||
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moduleclass = 'tools' |
45 changes: 45 additions & 0 deletions
45
easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb
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# Author: Denis Krišťák (INUITS) | ||
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easyblock = 'PythonBundle' | ||
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name = 'pyro-ppl' | ||
version = '1.9.0' | ||
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homepage = 'https://github.com/pyro-ppl/pyro' | ||
description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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dependencies = [ | ||
('Python', '3.11.3'), | ||
('SciPy-bundle', '2023.07'), | ||
('PyTorch', '2.1.2'), | ||
('tqdm', '4.66.1'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('opt-einsum', '3.3.0', { | ||
'source_tmpl': 'opt_einsum-%(version)s.tar.gz', | ||
'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], | ||
}), | ||
('pyro-api', '0.1.2', { | ||
'modulename': 'pyroapi', | ||
'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], | ||
}), | ||
(name, version, { | ||
'modulename': 'pyro', | ||
'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'], | ||
}), | ||
] | ||
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sanity_pip_check = True | ||
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sanity_check_commands = [ | ||
"python -c 'from pyroapi import distributions as dist'", | ||
"python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", | ||
"python -c 'from pyro import infer, nn, distributions'", | ||
] | ||
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moduleclass = 'tools' |