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{bio}[foss/2023a] dictys v1.1.0 w/ CUDA 12.1.1 #21166

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merged 4 commits into from
Aug 21, 2024
Merged

{bio}[foss/2023a] dictys v1.1.0 w/ CUDA 12.1.1 #21166

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78e994d
adding easyconfigs: dictys-1.1.0-foss-2023a.eb, dictys-1.1.0-foss-202…
pavelToman Aug 10, 2024
8f3466e
update junos-eznc version to fix tests failing
pavelToman Aug 10, 2024
9bbe333
separate econfig for junos-eznc with forked paramiko
pavelToman Aug 13, 2024
631f6a1
update junos-eznc.eb - pre- preinstallopts
pavelToman Aug 14, 2024
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102 changes: 102 additions & 0 deletions easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
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easyblock = 'PythonBundle'

name = 'dictys'
version = '1.1.0'
versionsuffix = '-CUDA-%(cudaver)s'

homepage = 'https://github.com/pinellolab/dictys'
description = "Context specific and dynamic gene regulatory network reconstruction and analysis."

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

builddependencies = [('poetry', '1.5.1')]
dependencies = [
('Python', '3.11.3'),
('CUDA', '12.1.1', '', SYSTEM),
('PyTorch-bundle', '2.1.2', versionsuffix),
('pybedtools', '0.9.1'),
('SAMtools', '1.18'),
('MACS2', '2.2.9.1'),
('FFmpeg', '6.0'),
('matplotlib', '3.7.2'),
('Python-bundle-PyPI', '2023.06'),
('SciPy-bundle', '2023.07'),
('networkx', '3.1'),
('h5py', '3.9.0'),
('pyro-ppl', '1.9.0', versionsuffix),
('adjustText', '0.7.3'),
('Pysam', '0.22.0'),
('paramiko', '3.2.0'),
('Jupyter-bundle', '20230823'),
('Qtconsole', '5.5.1'),
]

# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
local_pyDNase_preinstallopts = (
"cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && "
"sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && "
)

exts_list = [
('jupyter_console', '6.6.3', {
'source_tmpl': SOURCE_PY3_WHL,
'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
}),
('jupyter', '1.0.0', {
'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
}),
('args', '0.1.0', {
'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'],
}),
('clint', '0.5.1', {
'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'],
}),
('pynetbox', '7.4.0', {
'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
}),
('yamlordereddictloader', '0.4.2', {
'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
}),
('transitions', '0.9.2', {
'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
}),
('scp', '0.15.0', {
'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
}),
('pyserial', '3.5', {
'modulename': 'serial',
'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
}),
('ncclient', '0.6.15', {
'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
}),
('junos-eznc', '2.7.0', {
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'modulename': 'jnpr.junos',
'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
}),
('absl-py', '1.4.0', {
'modulename': 'absl',
'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
}),
('aerleon', '1.9.0', {
'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'],
}),
('homer', '0.7.0', {
'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'],
}),
('pyDNase', '0.3.0', {
'preinstallopts': local_pyDNase_preinstallopts,
'modulename': 'pyDNase',
'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'],
}),
(name, version, {
'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'],
}),
]

use_pip = True
sanity_pip_check = True

sanity_check_commands = ["dictys --help"]

moduleclass = 'bio'
100 changes: 100 additions & 0 deletions easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,100 @@
easyblock = 'PythonBundle'

name = 'dictys'
version = '1.1.0'

homepage = 'https://github.com/pinellolab/dictys'
description = "Context specific and dynamic gene regulatory network reconstruction and analysis."

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

builddependencies = [('poetry', '1.5.1')]
dependencies = [
('Python', '3.11.3'),
('PyTorch-bundle', '2.1.2'),
('pybedtools', '0.9.1'),
('SAMtools', '1.18'),
('MACS2', '2.2.9.1'),
('FFmpeg', '6.0'),
('matplotlib', '3.7.2'),
('Python-bundle-PyPI', '2023.06'),
('SciPy-bundle', '2023.07'),
('networkx', '3.1'),
('h5py', '3.9.0'),
('pyro-ppl', '1.9.0'),
('adjustText', '0.7.3'),
('Pysam', '0.22.0'),
('paramiko', '3.2.0'),
('Jupyter-bundle', '20230823'),
('Qtconsole', '5.5.1'),
]

# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
local_pyDNase_preinstallopts = (
"cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && "
"sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && "
)

exts_list = [
('jupyter_console', '6.6.3', {
'source_tmpl': SOURCE_PY3_WHL,
'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
}),
('jupyter', '1.0.0', {
'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
}),
('args', '0.1.0', {
'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'],
}),
('clint', '0.5.1', {
'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'],
}),
('pynetbox', '7.4.0', {
'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
}),
('yamlordereddictloader', '0.4.2', {
'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
}),
('transitions', '0.9.2', {
'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
}),
('scp', '0.15.0', {
'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
}),
('pyserial', '3.5', {
'modulename': 'serial',
'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
}),
('ncclient', '0.6.15', {
'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
}),
('junos-eznc', '2.7.0', {
'modulename': 'jnpr.junos',
'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
}),
('absl-py', '1.4.0', {
'modulename': 'absl',
'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
}),
('aerleon', '1.9.0', {
'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'],
}),
('homer', '0.7.0', {
'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'],
}),
('pyDNase', '0.3.0', {
'preinstallopts': local_pyDNase_preinstallopts,
'modulename': 'pyDNase',
'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'],
}),
(name, version, {
'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'],
}),
]

use_pip = True
sanity_pip_check = True

sanity_check_commands = ["dictys --help"]

moduleclass = 'bio'
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