From 86b254e89e7a28900e5f635a01850b3f49b8f9dd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Sat, 10 Aug 2024 14:11:43 +0200 Subject: [PATCH] #319 PR version --- 319_Dictys/dictys.eb | 58 +------------ 319_Dictys/dictys_CUDA.eb | 30 +------ 319_Dictys/dictys_comments.eb | 148 ++++++++++++++++++++++++++++++++++ 3 files changed, 150 insertions(+), 86 deletions(-) create mode 100644 319_Dictys/dictys_comments.eb diff --git a/319_Dictys/dictys.eb b/319_Dictys/dictys.eb index 4da27de..ad4ba02 100644 --- a/319_Dictys/dictys.eb +++ b/319_Dictys/dictys.eb @@ -8,48 +8,6 @@ description = "Context specific and dynamic gene regulatory network reconstructi toolchain = {'name': 'foss', 'version': '2023a'} -# 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 - builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), @@ -77,14 +35,6 @@ local_pyDNase_preinstallopts = ( "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " ) -# # 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 && " -# ) - exts_list = [ ('jupyter_console', '6.6.3', { 'source_tmpl': SOURCE_PY3_WHL, @@ -145,12 +95,6 @@ exts_list = [ use_pip = True sanity_pip_check = True -# sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] +sanity_check_commands = ["dictys --help"] moduleclass = 'bio' - -# 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" \ No newline at end of file diff --git a/319_Dictys/dictys_CUDA.eb b/319_Dictys/dictys_CUDA.eb index 851770d..e5988e7 100644 --- a/319_Dictys/dictys_CUDA.eb +++ b/319_Dictys/dictys_CUDA.eb @@ -9,26 +9,6 @@ description = "Context specific and dynamic gene regulatory network reconstructi toolchain = {'name': 'foss', 'version': '2023a'} -# 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 - builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), @@ -57,14 +37,6 @@ local_pyDNase_preinstallopts = ( "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " ) -# # 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 && " -# ) - exts_list = [ ('jupyter_console', '6.6.3', { 'source_tmpl': SOURCE_PY3_WHL, @@ -125,6 +97,6 @@ exts_list = [ use_pip = True sanity_pip_check = True -# sanity_check_commands = ["python -c 'from decaf import DECAF, DataModule'"] +sanity_check_commands = ["dictys --help"] moduleclass = 'bio' diff --git a/319_Dictys/dictys_comments.eb b/319_Dictys/dictys_comments.eb new file mode 100644 index 0000000..76652b5 --- /dev/null +++ b/319_Dictys/dictys_comments.eb @@ -0,0 +1,148 @@ +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'} + +# 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 + +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', '2.7.1', { + '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'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' + +# 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" \ No newline at end of file