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easyblock = 'PythonBundle' | ||
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name = 'dictys' | ||
version = '1.1.0' | ||
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homepage = 'https://github.com/pinellolab/dictys' | ||
description = "Context specific and dynamic gene regulatory network reconstruction and analysis." | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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# DEPS: | ||
# PyTorch OK | ||
# torchvision OK | ||
# torchaudio OK | ||
# homer ok | ||
# samtools OK | ||
# macs2 OK | ||
# ffmpeg OK | ||
# matplotlib OK | ||
# pyDNase ? ok | ||
# numpy','pandas', 'scipy' OK | ||
# 'docutils' ok pypi-b | ||
# 'h5py' OK | ||
# 'pyro-ppl' OK | ||
# 'networkx' OK | ||
# 'pybedtools', OK | ||
# 'threadpoolctl', 'joblib' OK pypi-b | ||
# 'adjustText' OK | ||
# 'jupyter' ok | ||
# homer 0.7.0 requires aerleon, ok | ||
# homer 0.7.0 requires junos-eznc, ok | ||
# homer 0.7.0 requires paramiko, OK | ||
# homer 0.7.0 requires pynetbox, ok | ||
# clint 0.5.1 requires args, ok | ||
# add ('Jupyter-bundle', '20230823'), instead of jupyter -> no add both | ||
# jupyter 1.0.0 requires ipykernel, which is not installed. | ||
# jupyter 1.0.0 requires ipywidgets, which is not installed. | ||
# jupyter 1.0.0 requires jupyter-console, which is not installed. | ||
# jupyter 1.0.0 requires nbconvert, which is not installed. | ||
# jupyter 1.0.0 requires notebook, which is not installed. | ||
# jupyter 1.0.0 requires qtconsole, which is not installed. | ||
# pydnase 0.3.0 has requirement matplotlib<2.0.0, but you have matplotlib 3.7.2. unpin - OK | ||
# dictys 1.1.0 requires jupyter, which is not installed. ok | ||
# junos-eznc 2.7.1 requires ncclient, ok | ||
# junos-eznc 2.7.1 requires pyserial, ok | ||
# junos-eznc 2.7.1 requires scp, ok | ||
# junos-eznc 2.7.1 requires transitions, ok | ||
# junos-eznc 2.7.1 requires yamlordereddictloader, ok | ||
# aerleon 1.9.0 has requirement absl-py<2.0.0,>=1.2.0, but you have absl-py 2.1.0. -> absl-py v1.4.0 | ||
# jupyter 1.0.0 requires jupyter-console, ok | ||
# jupyter 1.0.0 requires qtconsole, OK | ||
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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'), | ||
] | ||
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# 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 && " | ||
) | ||
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# # unpin dependencies versions - nor need anymore? | ||
# local_preinstallopts = ( | ||
# "sed -i" | ||
# " -e 's/networkx>=2.0,<3.0/networkx/'" | ||
# " -e 's/pytorch-lightning<2.0/pytorch-lightning/'" | ||
# " %(builddir)s/DECAFsyntheticdata/DECAF-%(version)s/requirements.txt && " | ||
# ) | ||
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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', '2.7.1', { | ||
'modulename': 'jnpr.junos', | ||
'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], | ||
}), | ||
('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'], | ||
}), | ||
] | ||
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use_pip = True | ||
sanity_pip_check = True | ||
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# sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] | ||
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moduleclass = 'bio' | ||
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# ERROR1: OK | ||
# -> WellingtonC.c - Generated by Cython 0.28.1 - I have 0.29.35 -> delete and cythonize -> local_pyDNase_preinstallopts | ||
# <- crash on PyDNase installation | ||
# pyDNase/footprinting/WellingtonC.c:181:12: fatal error: longintrepr.h: No such file or directory | ||
# 181 | #include "longintrepr.h" |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,130 @@ | ||
easyblock = 'PythonBundle' | ||
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||
name = 'dictys' | ||
version = '1.1.0' | ||
versionsuffix = '-CUDA-%(cudaver)s' | ||
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homepage = 'https://github.com/pinellolab/dictys' | ||
description = "Context specific and dynamic gene regulatory network reconstruction and analysis." | ||
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toolchain = {'name': 'foss', 'version': '2023a'} | ||
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# DEPS: | ||
# PyTorch OK | ||
# torchvision OK | ||
# torchaudio OK | ||
# homer ok | ||
# samtools OK | ||
# macs2 OK | ||
# ffmpeg OK | ||
# matplotlib OK | ||
# pyDNase ? ok | ||
# numpy','pandas', 'scipy' OK | ||
# 'docutils' ok pypi-b | ||
# 'h5py' OK | ||
# 'pyro-ppl' OK | ||
# 'networkx' OK | ||
# 'pybedtools', OK | ||
# 'threadpoolctl', 'joblib' OK pypi-b | ||
# 'adjustText' OK | ||
# 'jupyter' ok | ||
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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'), | ||
] | ||
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# 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 && " | ||
) | ||
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# # unpin dependencies versions - nor need anymore? | ||
# local_preinstallopts = ( | ||
# "sed -i" | ||
# " -e 's/networkx>=2.0,<3.0/networkx/'" | ||
# " -e 's/pytorch-lightning<2.0/pytorch-lightning/'" | ||
# " %(builddir)s/DECAFsyntheticdata/DECAF-%(version)s/requirements.txt && " | ||
# ) | ||
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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', '2.7.1', { | ||
'modulename': 'jnpr.junos', | ||
'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], | ||
}), | ||
('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'], | ||
}), | ||
] | ||
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use_pip = True | ||
sanity_pip_check = True | ||
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# sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] | ||
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moduleclass = 'bio' |