From 9014005b0bf858c550ee150b08f316e7ea48854f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 11 Mar 2024 15:31:32 +0100 Subject: [PATCH 1/5] adding easyconfigs: pySCENIC-0.12.1-foss-2023a.eb --- .../p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..e006374a05a --- /dev/null +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'pySCENIC' +version = '0.12.1' +local_commit = '31d51a1' + +homepage = 'https://github.com/aertslab/pySCENIC' +description = """pySCENIC is a lightning-fast python implementation of the SCENIC +pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables +biologists to infer transcription factors, gene regulatory networks and +cell types from single-cell RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('Arrow', '14.0.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('networkx', '3.1'), + ('dask', '2023.12.1'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('multiprocessing_on_dill', '3.5.0a4', { + 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], + }), + ('frozendict', '2.4.0', { + 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], + }), + ('arboreto', '0.1.6', { + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('boltons', '23.1.1', { + 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], + }), + ('interlap', '0.2.7', { + 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], + }), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('pyscenic', version, { + # download from commit to get fix for numpy error + # https://github.com/aertslab/pySCENIC/issues/518 + 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], + 'sources': [{ + 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyscenic'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyscenic --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From f0f07906e2981283fe48825bcd6f69fc1b32bd0d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 11 Mar 2024 16:10:28 +0100 Subject: [PATCH 2/5] fix filename --- easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb index e006374a05a..8f05d25d9c0 100644 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], 'sources': [{ 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz' + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit }], 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], }), From 8f52e90a4ed0e5b2983250bab91bddc958c6928b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 12 Mar 2024 10:57:35 +0100 Subject: [PATCH 3/5] update version with date --- .../pySCENIC-0.12.1-20240311-foss-2023a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb new file mode 100644 index 00000000000..2e5e8193e0d --- /dev/null +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'pySCENIC' +version = '0.12.1-20240311' +local_commit = '31d51a1' + +homepage = 'https://github.com/aertslab/pySCENIC' +description = """pySCENIC is a lightning-fast python implementation of the SCENIC +pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables +biologists to infer transcription factors, gene regulatory networks and +cell types from single-cell RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('Arrow', '14.0.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('networkx', '3.1'), + ('dask', '2023.12.1'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('multiprocessing_on_dill', '3.5.0a4', { + 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], + }), + ('frozendict', '2.4.0', { + 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], + }), + ('arboreto', '0.1.6', { + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('boltons', '23.1.1', { + 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], + }), + ('interlap', '0.2.7', { + 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], + }), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('pyscenic', '0.12.1', { + # download from commit to get fix for numpy error + # https://github.com/aertslab/pySCENIC/issues/518 + 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], + 'sources': [{ + 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit + }], + 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyscenic'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyscenic --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From cb9d08666e88d9fec28815dac96db81c536c7e39 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 14 Mar 2024 13:43:58 +0100 Subject: [PATCH 4/5] Delete easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb --- .../p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 77 ------------------- 1 file changed, 77 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb deleted file mode 100644 index 8f05d25d9c0..00000000000 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb +++ /dev/null @@ -1,77 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pySCENIC' -version = '0.12.1' -local_commit = '31d51a1' - -homepage = 'https://github.com/aertslab/pySCENIC' -description = """pySCENIC is a lightning-fast python implementation of the SCENIC -pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables -biologists to infer transcription factors, gene regulatory networks and -cell types from single-cell RNA-seq data.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('PyYAML', '6.0'), - ('Arrow', '14.0.1'), - ('scikit-learn', '1.3.1'), - ('tqdm', '4.66.1'), - ('networkx', '3.1'), - ('dask', '2023.12.1'), - ('aiohttp', '3.8.5'), - ('dill', '0.3.7'), - ('loompy', '3.0.7'), - ('umap-learn', '0.5.5'), -] - -use_pip = True - -exts_list = [ - ('cytoolz', '0.12.3', { - 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], - }), - ('multiprocessing_on_dill', '3.5.0a4', { - 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], - }), - ('frozendict', '2.4.0', { - 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], - }), - ('arboreto', '0.1.6', { - 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], - }), - ('boltons', '23.1.1', { - 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], - }), - ('interlap', '0.2.7', { - 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], - }), - ('ctxcore', '0.2.0', { - 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], - 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], - }), - ('pyscenic', version, { - # download from commit to get fix for numpy error - # https://github.com/aertslab/pySCENIC/issues/518 - 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], - 'sources': [{ - 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', - 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit - }], - 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], - }), -] - -sanity_check_paths = { - 'files': ['bin/pyscenic'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["pyscenic --help"] - -sanity_pip_check = True - -moduleclass = 'bio' From 96343840cdb4480c3ae12eaa662aa4a0445d550b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 18 Mar 2024 19:16:58 +0100 Subject: [PATCH 5/5] Update dask version to be same as for another modules --- .../p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb index 2e5e8193e0d..2842812499f 100644 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb @@ -19,7 +19,7 @@ dependencies = [ ('scikit-learn', '1.3.1'), ('tqdm', '4.66.1'), ('networkx', '3.1'), - ('dask', '2023.12.1'), + ('dask', '2023.9.2'), ('aiohttp', '3.8.5'), ('dill', '0.3.7'), ('loompy', '3.0.7'),