From 78e994dc672538f7e25eaef61133540049d97ad5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Sat, 10 Aug 2024 14:12:46 +0200 Subject: [PATCH 1/4] adding easyconfigs: dictys-1.1.0-foss-2023a.eb, dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb --- .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 102 ++++++++++++++++++ .../d/dictys/dictys-1.1.0-foss-2023a.eb | 100 +++++++++++++++++ 2 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..e5988e75d30 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,102 @@ +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', '2.7.1', { + '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' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..ad4ba02e66d --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -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', '2.7.1', { + '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' From 8f3466efeb0af98784fbcd1db69657f2f3c51f84 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Sat, 10 Aug 2024 16:08:26 +0200 Subject: [PATCH 2/4] update junos-eznc version to fix tests failing --- .../d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 4 ++-- easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb index e5988e75d30..de99e242d09 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -70,9 +70,9 @@ exts_list = [ ('ncclient', '0.6.15', { 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], }), - ('junos-eznc', '2.7.1', { + ('junos-eznc', '2.7.0', { 'modulename': 'jnpr.junos', - 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], }), ('absl-py', '1.4.0', { 'modulename': 'absl', diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb index ad4ba02e66d..e0fa2174545 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -68,9 +68,9 @@ exts_list = [ ('ncclient', '0.6.15', { 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], }), - ('junos-eznc', '2.7.1', { + ('junos-eznc', '2.7.0', { 'modulename': 'jnpr.junos', - 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + 'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'], }), ('absl-py', '1.4.0', { 'modulename': 'absl', From 9bbe3338d0303e80359a2b41e8f3cac30170b0c6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 13 Aug 2024 16:14:24 +0200 Subject: [PATCH 3/4] separate econfig for junos-eznc with forked paramiko --- .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb | 21 +------ .../d/dictys/dictys-1.1.0-foss-2023a.eb | 21 +------ .../junos-eznc-2.7.1-GCCcore-12.3.0.eb | 56 +++++++++++++++++++ 3 files changed, 58 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb index de99e242d09..f04774b1b55 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -29,6 +29,7 @@ dependencies = [ ('paramiko', '3.2.0'), ('Jupyter-bundle', '20230823'), ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), ] # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version @@ -54,26 +55,6 @@ exts_list = [ ('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'], diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb index e0fa2174545..0b97a82cfde 100644 --- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -27,6 +27,7 @@ dependencies = [ ('paramiko', '3.2.0'), ('Jupyter-bundle', '20230823'), ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), ] # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version @@ -52,26 +53,6 @@ exts_list = [ ('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'], diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2799845eb24 --- /dev/null +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'junos-eznc' +version = '2.7.1' + +homepage = 'https://github.com/Juniper/py-junos-eznc' +description = "Python library for Junos automation." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('PyYAML', '6.0'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py +local_preinstallopts = "sed -i '6d' setup.py && " + +exts_list = [ + ('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'], + }), + ('paramiko', '3.4.0', { + # Juniper fork of paramiko - compatible with junos-eznc + 'source_urls': ['https://github.com/Juniper/paramiko/archive/'], + 'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}], + 'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'], + }), + (name, version, { + 'modulename': 'jnpr.junos', + 'preinstallopts': "sed -i '6d' setup.py && ", + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 631f6a1d3b69d86783db82edde4c8d81a2ca022a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Aug 2024 10:02:04 +0200 Subject: [PATCH 4/4] update junos-eznc.eb - pre- preinstallopts --- .../j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb index 2799845eb24..ceaec648de3 100644 --- a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -17,9 +17,6 @@ dependencies = [ ('bcrypt', '4.0.1'), ] -# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py -local_preinstallopts = "sed -i '6d' setup.py && " - exts_list = [ ('yamlordereddictloader', '0.4.2', { 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], @@ -45,7 +42,8 @@ exts_list = [ }), (name, version, { 'modulename': 'jnpr.junos', - 'preinstallopts': "sed -i '6d' setup.py && ", + # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py + 'preinstallopts': "sed -i '/pip install/d' setup.py && ", 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], }), ]