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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| 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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||
| 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 = ["dictys --help"] | ||
|
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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" |