Skip to content

Commit

Permalink
Merge pull request #20551 from pavelToman/20240517134249_new_pr_CellB…
Browse files Browse the repository at this point in the history
…ender030

{tools}[foss/2023a] CellBender v0.3.0, jupyter-contrib-nbextensions v0.7.0, pyro-ppl v1.9.0
  • Loading branch information
boegel committed Jun 4, 2024
2 parents b962b77 + c5b7f04 commit 62af27c
Show file tree
Hide file tree
Showing 5 changed files with 296 additions and 0 deletions.
Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
easyblock = 'PythonBundle'

name = 'CellBender'
version = '0.3.0'
versionsuffix = '-CUDA-%(cudaver)s'

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.
"""

toolchain = {'name': 'foss', 'version': '2023a'}

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'),
]

use_pip = True

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'],
}),
]

sanity_check_paths = {
'files': ['bin/cellbender'],
'dirs': ['lib/python%(pyshortver)s/site-packages'],
}

sanity_check_commands = [
"cellbender --help",
]

sanity_pip_check = True

moduleclass = 'bio'
70 changes: 70 additions & 0 deletions easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
easyblock = 'PythonBundle'

name = 'CellBender'
version = '0.3.0'

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.
"""

toolchain = {'name': 'foss', 'version': '2023a'}

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'),
]

use_pip = True

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'],
}),
]

sanity_check_paths = {
'files': ['bin/cellbender'],
'dirs': ['lib/python%(pyshortver)s/site-packages'],
}

sanity_check_commands = [
"cellbender --help",
]

sanity_pip_check = True

moduleclass = 'bio'
Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
easyblock = "PythonBundle"

name = 'jupyter-contrib-nbextensions'
version = '0.7.0'

homepage = 'https://github.com/ipython-contrib/jupyter_contrib_nbextensions'
description = 'A collection of various notebook extensions for Jupyter'

toolchain = {'name': 'GCCcore', 'version': '12.3.0'}

builddependencies = [
('binutils', '2.40'),
('nodejs', '18.17.1'),
]

dependencies = [
('Python', '3.11.3'),
('IPython', '8.14.0'),
('PyYAML', '6.0'),
('jupyter-server', '2.7.2'),
]

use_pip = True

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'],
}),
]

sanity_pip_check = True

sanity_check_paths = {
'files': ['bin/jupyter-contrib', 'bin/jupyter-contrib-nbextension', 'bin/jupyter-nbextensions_configurator'],
'dirs': ['lib64/python%(pyshortver)s/site-packages']
}

moduleclass = 'tools'
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
# Author: Denis Krišťák (INUITS)

easyblock = 'PythonBundle'

name = 'pyro-ppl'
version = '1.9.0'
versionsuffix = '-CUDA-%(cudaver)s'

homepage = 'https://github.com/pyro-ppl/pyro'
description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."

toolchain = {'name': 'foss', 'version': '2023a'}

dependencies = [
('CUDA', '12.1.1', '', SYSTEM),
('Python', '3.11.3'),
('SciPy-bundle', '2023.07'),
('PyTorch', '2.1.2', versionsuffix),
('tqdm', '4.66.1'),
]

use_pip = True

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'],
}),
]

sanity_pip_check = True

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'",
]

moduleclass = 'tools'
45 changes: 45 additions & 0 deletions easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
# Author: Denis Krišťák (INUITS)

easyblock = 'PythonBundle'

name = 'pyro-ppl'
version = '1.9.0'

homepage = 'https://github.com/pyro-ppl/pyro'
description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."

toolchain = {'name': 'foss', 'version': '2023a'}

dependencies = [
('Python', '3.11.3'),
('SciPy-bundle', '2023.07'),
('PyTorch', '2.1.2'),
('tqdm', '4.66.1'),
]

use_pip = True

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'],
}),
]

sanity_pip_check = True

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'",
]

moduleclass = 'tools'

0 comments on commit 62af27c

Please sign in to comment.