From d235a77e00829ca0e0fa6357454119bea5068a16 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Mon, 27 May 2024 12:10:59 +0200 Subject: [PATCH 01/25] easyconfigs for chrombpnet and its dependencies --- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 38 ++++++++++ .../c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb | 38 ++++++++++ .../chrombpnet/chrombpnet-0.1.7-foss-2021b.eb | 71 ++++++++++++++++++ .../c/coverage/coverage-6.4-GCCcore-11.2.0.eb | 35 +++++++++ .../d/deepdish/deepdish-0.3.7-foss-2021b.eb | 32 ++++++++ .../hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb | 34 +++++++++ .../kundajelab-shap-1-foss-2021b | 49 +++++++++++++ .../m/modisco-lite/modisco-lite-foss-2021b | 62 ++++++++++++++++ .../m/modisco/modisco-0.5.16.0-foss-2021b | 57 +++++++++++++++ .../n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb | 36 +++++++++ .../setuptools-54.2.0-GCCcore-11.2.0.eb | 26 +++++++ .../w/WeasyPrint/WeasyPrint-52.2-foss-2021b | 73 +++++++++++++++++++ .../x/XGBoost/XGBoost-1.6.1-foss-2021b.eb | 29 ++++++++ 13 files changed, 580 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb create mode 100644 easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b create mode 100644 easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b create mode 100644 easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b create mode 100644 easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb new file mode 100644 index 00000000000..e6ae64b2983 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.2' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('Pillow', '8.3.2'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + (name, version, { + 'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' \ No newline at end of file diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6a0d9c64671 --- /dev/null +++ b/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'cffi' +version = '1.14.5' + +homepage = 'https://cffi.readthedocs.io/en/latest/' +description = """C Foreign Function Interface for Python. Interact with almost any C code from +Python, based on C-like declarations that you can often copy-paste from header +files or documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + (name, version, { + 'checksums': ['fd78e5fee591709f32ef6edb9a015b4aa1a5022598e36227500c8f4e02328d9c'], + }), +] + +moduleclass = 'tools' \ No newline at end of file diff --git a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb new file mode 100644 index 00000000000..1df5364e95f --- /dev/null +++ b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'chrombpnet' +version = '0.1.7' + +homepage = 'https://github.com/kundajelab/chrombpnet' +description = """ ChromBPNet is a fully convolutional neural network that uses dilated convolutions with residual connections to enable large receptive fields with efficient parameterization. It also performs automatic assay bias correction. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('SAMtools', '1.15.1'), + ('BEDTools', '2.30.0'), + ('Kent_tools', '422'), + ('pyBigWig', '0.3.18'), + ('MEME', '5.4.1'), + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('pyfaidx', '0.7.0'), + ('deepdish', '0.3.7'), + ('matplotlib', '3.4.3'), + ('modisco', '0.5.16.0'), + ('modisco-lite', '2.0.7'), + ('scikit-learn', '1.0.2'), + ('TensorFlow', '2.8.4'), + ('tensorflow-probability', '0.16.0'), + ('protobuf-python', '3.17.3'), + ('tqdm', '4.62.3'), + ('kundajelab-shap', '1'), + ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 + ('WeasyPrint', '52.5'), +] + +use_pip = True + +# Loosen unnecessarily strict version dependencies +local_preinstallopts = "sed -i 's|pyfaidx==|pyfaidx>=|g' requirements.txt && " +local_preinstallopts += "sed -i 's|scikit-learn>=1.1.2|scikit-learn>=1.0.0|g' requirements.txt && " +local_preinstallopts += "sed -i 's|tensorflow==|tensorflow>=|g' requirements.txt && " +local_preinstallopts += "sed -i 's|tensorflow-probability==|tensorflow-probability>=|g' requirements.txt && " +local_preinstallopts += "sed -i 's|protobuf==3.20|protobuf>=3.17.0|g' requirements.txt && " +local_preinstallopts += "sed -i 's|tqdm==|tqdm>=|g' requirements.txt && " +local_preinstallopts += "sed -i 's|numpy== 1.23.4|numpy>=1.21.0|g' requirements.txt && " + +exts_list = [ + ( 'matplotlib-venn', '0.11.6', { + 'checksums': ['d209a9845bb3a54c4247f1ef3f745e4819660ecc9208137097d2a51281f2a478'], + }), + ('tensorflow-estimator', '2.8.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], + }), + ( 'deeplift', '0.6.13.0', { + 'checksums': ['354ac5a00630b2df0856e8c948262e38c7eb83a719f71d6b5bf8ec4b064cb432'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['e5fae544d8e533d770c72313b9902097ffd32ef66d5962e90546c3cd9ecce759'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chrombpnet'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["chrombpnet --help"] + +sanity_pip_check = True + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bb0a3ee38aa --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '6.4' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['727dafd7f67a6e1cad808dc884bd9c5a2f6ef1f8f6d2f22b37b96cb0080d4f49'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["coverage --help"] + +moduleclass = 'tools' \ No newline at end of file diff --git a/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb b/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb new file mode 100644 index 00000000000..5580169c0a0 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'deepdish' +version = '0.3.7' + +homepage = 'https://github.com/uchicago-cs/deepdish' +description = """Flexible HDF5 saving/loading and other +data science tools from the University of Chicago.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6aff3abef693cec34438f183f29d1a2d9862aba27bb959d4f24d56e007e41ff3'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-image', '0.19.1'), + ('PyTables', '3.6.1'), +] + +preinstallopts = """python setup.py build && """ + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'data' \ No newline at end of file diff --git a/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb b/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb new file mode 100644 index 00000000000..cd36faf7f13 --- /dev/null +++ b/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'hdf5plugin' +version = '3.2.0' + +homepage = "https://github.com/silx-kit/hdf5plugin" +description = """hdf5plugin provides HDF5 compression filters +(namely: Blosc, Blosc2, BitShuffle, BZip2, FciDecomp, LZ4, SZ, +SZ3, Zfp, ZStd) and makes them usable from h5py.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('h5py', '3.6.0'), + ('py-cpuinfo', '9.0.0'), + ('Python', '3.9.6'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['8900ab06df2a20f88c9c56ecf45a99655e08ba4d730706f8798b4ea2158b291a'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + +moduleclass = 'data' \ No newline at end of file diff --git a/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b new file mode 100644 index 00000000000..05da9533301 --- /dev/null +++ b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'kundajelab-shap' +version = '1' + +homepage = "https://github.com/kundajelab/shap" +description = """This is a custom fork of the shap repository that has support +for computing hypothetical importance scores, for use with TF-MoDISco. +It was originally forked under AvantiShri/shap.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('matplotlib', '3.4.3'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.2'), + ('scikit-image', '0.19.1'), + ('tqdm', '4.62.3'), + ('numba', '0.54.1'), + ('nose3', '1.3.8'), + ('XGBoost', '1.6.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + ('lightgbm', '3.3.2', { + 'checksums': ['5d25d16e77c844c297ece2044df57651139bc3c8ad8c4108916374267ac68b64'], + }), + (name, version, { + 'modulename': 'shap', + 'checksums': ['0269759677ae8a71544e34168c680588703c2e983a20ff8bce93cd73dc6004ff'], + }), +] + +moduleclass = 'data' \ No newline at end of file diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b new file mode 100644 index 00000000000..5b30245e373 --- /dev/null +++ b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'modisco-lite' +version = '2.0.7' + +homepage = 'https://github.com/jmschrei/tfmodisco-lite' +description = """TF-MoDISco is a motif detection algorithm that takes in nucleotide + sequence and the attributions from a neural network model and return motifs + that are repeatedly enriched for attriution score across the examples. + This tool will take in one-hot encoded sequence, the corresponding + attribution scores, and a few other parameters, and return the motifs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('h5py', '3.6.0'), + ('hdf5plugin', '3.2.0'), + ('igraph', '0.9.5'), + ('python-igraph', '0.9.8'), + ('leidenalg', '0.8.8'), + ('matplotlib', '3.4.3'), + ('numba', '0.54.1'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 + ('scikit-learn', '1.0.2'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +# Loosen unnecessarily strict version dependencies +local_preinstallopts = "sed -i 's|numpy >= 1.21.5|numpy >= 1.21.3|g' setup.py && " +local_preinstallopts += "sed -i 's|pandas >= 1.4.3|pandas >= 1.3.4|g' setup.py && " +local_preinstallopts += "sed -i 's|leidenalg == 0.8.10|leidenalg >= 0.8.8|g' setup.py && " +local_preinstallopts += "sed -i 's|igraph == 0.9.11|igraph >= 0.9.5|g' setup.py && " +local_preinstallopts += "sed -i 's|h5py >= 3.7.0|h5py >= 3.6.0|g' setup.py && " + +exts_list = [ + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + (name, version, { + 'modulename': 'modiscolite', + 'preinstallopts': local_preinstallopts, + 'checksums': ['937a570cd0b5cff67daddb05215f5ee4820b2f67bf8bb0e2088424a217953eef'], + }), +] + +sanity_check_paths = { + 'files': ['bin/modisco'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +sanity_check_commands = [ + "modisco -h", + "modisco motifs -h", + "modisco report -h", +] + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b new file mode 100644 index 00000000000..c4169295732 --- /dev/null +++ b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'modisco' +version = '0.5.16.0' + +homepage = 'https://github.com/kundajelab/tfmodisco' +description = """TF-MoDISco: Transcription-Factor Motif Discovery from Importance Scores.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('h5py', '3.6.0'), + ('igraph', '0.9.5'), + ('leidenalg', '0.8.8'), + ('matplotlib', '3.4.3'), + ('numba', '0.54.1'), # for pynndescent + ('psutil', '5.9.4'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 + ('scikit-learn', '1.0.2'), + ('tqdm', '4.62.3'), + ('TensorFlow', '2.8.4'), +] + +use_pip = True + +exts_list = [ + ('joblib', '1.0.1', { + 'checksums': ['9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7'], + }), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), + (name, version, { + 'checksums': ['24d1eef8f7e3617a8da7e595252fe9f5a20803b79453a8d11132769f04f49085'], + # Loosen unnecessarily strict version dependency for numpy + 'preinstallopts': "sed -i 's|numpy>=1.9|numpy>=1.2|g' setup.py &&", + 'postinstallcmds': ["cp -a test %(installdir)s"], + }), +] + +sanity_check_paths = { + 'files': ['bin/run_leiden'], + 'dirs': ['test', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'from modisco import core' " + # copy test to build directory, after making sure it exists, so --sanity-check-only works; + # enable write permissions, since installation directory may be read-only + "mkdir -p %(builddir)s && cp -a %(installdir)s/test %(builddir)s/ && chmod -R u+wx %(builddir)s/test", + "cd %(builddir)s/test && python test_core.py && python test_tfmodisco_workflow.py", +] + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0f868319ebf --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('coverage', '6.4'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +options = {'modulename': 'nose'} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6ac146e203c --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'setuptools' +version = '54.2.0' + +homepage = "https://pypi.org/project/setuptools" +description = """Easily download, build, install, upgrade, and uninstall Python packages""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['aa9c24fb83a9116b8d425e53bec24c7bfdbffc313c2159f9ed036d4a6dd32d7d'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b new file mode 100644 index 00000000000..c7bc833518b --- /dev/null +++ b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'WeasyPrint' +version = '52.5' + +homepage = 'https://github.com/Kozea/WeasyPrint' +description = """WeasyPrint is a smart solution helping web developers to create +PDF documents. It turns simple HTML pages into gorgeous statistical reports, +invoices, tickets.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('cairo', '1.16.0'), + ('setuptools', '54.2.0'), + ('cffi', '1.14.5'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), +] + +use_pip = True + +exts_list = [ + ('cssselect2', '0.4.1', { + 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], + }), + ('cairocffi', '1.2.0', { + 'modulename': 'cairocffi', + 'source_tmpl': 'cairocffi-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], + 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], + }), + ('CairoSVG', '2.5.1', { + 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('tinycss2', '1.1.0', { + 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], + }), + ('pydyf', '0.0.2', { + 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], + }), + ('pyphen', '0.10.0', { + 'modulename': 'pyphen', + 'source_tmpl': 'Pyphen-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], + 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], + }), + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + (name, version, { + 'modulename': 'weasyprint', + 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], + }), +] + +sanity_check_paths = { + 'files': ['bin/weasyprint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["weasyprint --help"] + +sanity_pip_check = True + +moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb new file mode 100644 index 00000000000..89bbf23d8a0 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.6.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24072028656f3428e7b8aabf77340ece057f273e41f7f85d67ccaefb7454bb18'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' \ No newline at end of file From bf599312d0527c97dc7f90bba74d804360aeffd6 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Thu, 30 May 2024 17:09:05 +0200 Subject: [PATCH 02/25] Fix name extension for WeasyPrint easyconfig --- .../WeasyPrint/WeasyPrint-52.2-foss-2021b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb new file mode 100644 index 00000000000..c7bc833518b --- /dev/null +++ b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'WeasyPrint' +version = '52.5' + +homepage = 'https://github.com/Kozea/WeasyPrint' +description = """WeasyPrint is a smart solution helping web developers to create +PDF documents. It turns simple HTML pages into gorgeous statistical reports, +invoices, tickets.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('cairo', '1.16.0'), + ('setuptools', '54.2.0'), + ('cffi', '1.14.5'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), +] + +use_pip = True + +exts_list = [ + ('cssselect2', '0.4.1', { + 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], + }), + ('cairocffi', '1.2.0', { + 'modulename': 'cairocffi', + 'source_tmpl': 'cairocffi-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], + 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], + }), + ('CairoSVG', '2.5.1', { + 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('tinycss2', '1.1.0', { + 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], + }), + ('pydyf', '0.0.2', { + 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], + }), + ('pyphen', '0.10.0', { + 'modulename': 'pyphen', + 'source_tmpl': 'Pyphen-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], + 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], + }), + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + (name, version, { + 'modulename': 'weasyprint', + 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], + }), +] + +sanity_check_paths = { + 'files': ['bin/weasyprint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["weasyprint --help"] + +sanity_pip_check = True + +moduleclass = 'lib' \ No newline at end of file From 0ad42588939c123cba793f5c792e94a127b63a69 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 07:47:47 +0200 Subject: [PATCH 03/25] Fix version in name for WeasyPrint easyconfig --- .../WeasyPrint/WeasyPrint-52.5-foss-2021b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb new file mode 100644 index 00000000000..c7bc833518b --- /dev/null +++ b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'WeasyPrint' +version = '52.5' + +homepage = 'https://github.com/Kozea/WeasyPrint' +description = """WeasyPrint is a smart solution helping web developers to create +PDF documents. It turns simple HTML pages into gorgeous statistical reports, +invoices, tickets.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('cairo', '1.16.0'), + ('setuptools', '54.2.0'), + ('cffi', '1.14.5'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), +] + +use_pip = True + +exts_list = [ + ('cssselect2', '0.4.1', { + 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], + }), + ('cairocffi', '1.2.0', { + 'modulename': 'cairocffi', + 'source_tmpl': 'cairocffi-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], + 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], + }), + ('CairoSVG', '2.5.1', { + 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('tinycss2', '1.1.0', { + 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], + }), + ('pydyf', '0.0.2', { + 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], + }), + ('pyphen', '0.10.0', { + 'modulename': 'pyphen', + 'source_tmpl': 'Pyphen-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], + 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], + }), + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + (name, version, { + 'modulename': 'weasyprint', + 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], + }), +] + +sanity_check_paths = { + 'files': ['bin/weasyprint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["weasyprint --help"] + +sanity_pip_check = True + +moduleclass = 'lib' \ No newline at end of file From 103dbf120d085ae0074dbc74ee9fe690e7660409 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 11:03:18 +0200 Subject: [PATCH 04/25] bokeh with tornado 6.2 --- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 38 ------------------- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 2 +- 2 files changed, 1 insertion(+), 39 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb deleted file mode 100644 index 34b3817fed0..00000000000 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '2.4.2' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('PyYAML', '5.4.1'), - ('Pillow', '8.3.2'), - ('SciPy-bundle', '2021.10'), -] - -use_pip = True - -exts_list = [ - ('tornado', '6.1', { - 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], - }), - (name, version, { - 'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'], - }), -] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["bokeh --help"] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb index e6ae64b2983..9b485eb958a 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb @@ -35,4 +35,4 @@ sanity_check_paths = { sanity_check_commands = ["bokeh --help"] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From 9dd2347777ebe8801119bb2fab0040527b655699 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 11:04:35 +0200 Subject: [PATCH 05/25] Fixing test errors --- .../c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb | 2 +- .../chrombpnet/chrombpnet-0.1.7-foss-2021b.eb | 20 ++--- .../c/coverage/coverage-6.4-GCCcore-11.2.0.eb | 2 +- .../d/deepdish/deepdish-0.3.7-foss-2021b.eb | 4 +- .../hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb | 6 +- ...-2021b => kundajelab-shap-1-foss-2021b.eb} | 6 +- ...-foss-2021b => modisco-lite-foss-2021b.eb} | 14 ++-- ...s-2021b => modisco-0.5.16.0-foss-2021b.eb} | 10 +-- .../n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb | 2 +- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 39 ---------- .../setuptools-54.2.0-GCCcore-11.2.0.eb | 2 +- .../w/WeasyPrint/WeasyPrint-52.2-foss-2021b | 73 ------------------- .../WeasyPrint/WeasyPrint-52.2-foss-2021b.eb | 73 ------------------- .../WeasyPrint/WeasyPrint-52.5-foss-2021b.eb | 36 ++++----- .../x/XGBoost/XGBoost-1.6.1-foss-2021b.eb | 2 +- 15 files changed, 53 insertions(+), 238 deletions(-) rename easybuild/easyconfigs/k/kundajelab-shap/{kundajelab-shap-1-foss-2021b => kundajelab-shap-1-foss-2021b.eb} (96%) rename easybuild/easyconfigs/m/modisco-lite/{modisco-lite-foss-2021b => modisco-lite-foss-2021b.eb} (92%) rename easybuild/easyconfigs/m/modisco/{modisco-0.5.16.0-foss-2021b => modisco-0.5.16.0-foss-2021b.eb} (96%) delete mode 100644 easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb delete mode 100644 easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b delete mode 100644 easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb index 6a0d9c64671..062c8dac76e 100644 --- a/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cffi/cffi-1.14.5-GCCcore-11.2.0.eb @@ -35,4 +35,4 @@ exts_list = [ }), ] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb index 1df5364e95f..7aa658e4dc7 100644 --- a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb @@ -14,18 +14,18 @@ dependencies = [ ('Kent_tools', '422'), ('pyBigWig', '0.3.18'), ('MEME', '5.4.1'), - ('Python', '3.9.6'), + ('Python', '3.9.6'), ('h5py', '3.6.0'), - ('pyfaidx', '0.7.0'), - ('deepdish', '0.3.7'), + ('pyfaidx', '0.7.0'), + ('deepdish', '0.3.7'), ('matplotlib', '3.4.3'), ('modisco', '0.5.16.0'), ('modisco-lite', '2.0.7'), - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.2'), ('TensorFlow', '2.8.4'), - ('tensorflow-probability', '0.16.0'), - ('protobuf-python', '3.17.3'), - ('tqdm', '4.62.3'), + ('tensorflow-probability', '0.16.0'), + ('protobuf-python', '3.17.3'), + ('tqdm', '4.62.3'), ('kundajelab-shap', '1'), ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 ('WeasyPrint', '52.5'), @@ -44,7 +44,7 @@ local_preinstallopts += "sed -i 's|numpy== 1.23.4|numpy>=1.21.0|g' requirements. exts_list = [ ( 'matplotlib-venn', '0.11.6', { - 'checksums': ['d209a9845bb3a54c4247f1ef3f745e4819660ecc9208137097d2a51281f2a478'], + 'checksums': ['d209a9845bb3a54c4247f1ef3f745e4819660ecc9208137097d2a51281f2a478'], }), ('tensorflow-estimator', '2.8.0', { 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', @@ -52,7 +52,7 @@ exts_list = [ }), ( 'deeplift', '0.6.13.0', { 'checksums': ['354ac5a00630b2df0856e8c948262e38c7eb83a719f71d6b5bf8ec4b064cb432'], - }), + }), (name, version, { 'preinstallopts': local_preinstallopts, 'checksums': ['e5fae544d8e533d770c72313b9902097ffd32ef66d5962e90546c3cd9ecce759'], @@ -68,4 +68,4 @@ sanity_check_commands = ["chrombpnet --help"] sanity_pip_check = True -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb index bb0a3ee38aa..272cf434036 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-6.4-GCCcore-11.2.0.eb @@ -32,4 +32,4 @@ sanity_check_paths = { sanity_check_commands = ["coverage --help"] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb b/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb index 5580169c0a0..c8933b4e3e1 100644 --- a/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb +++ b/easybuild/easyconfigs/d/deepdish/deepdish-0.3.7-foss-2021b.eb @@ -4,7 +4,7 @@ name = 'deepdish' version = '0.3.7' homepage = 'https://github.com/uchicago-cs/deepdish' -description = """Flexible HDF5 saving/loading and other +description = """Flexible HDF5 saving/loading and other data science tools from the University of Chicago.""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -29,4 +29,4 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb b/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb index cd36faf7f13..0986ce5efd9 100644 --- a/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/h/hdf5plugin/hdf5plugin-3.2.0-foss-2021b.eb @@ -4,8 +4,8 @@ name = 'hdf5plugin' version = '3.2.0' homepage = "https://github.com/silx-kit/hdf5plugin" -description = """hdf5plugin provides HDF5 compression filters -(namely: Blosc, Blosc2, BitShuffle, BZip2, FciDecomp, LZ4, SZ, +description = """hdf5plugin provides HDF5 compression filters +(namely: Blosc, Blosc2, BitShuffle, BZip2, FciDecomp, LZ4, SZ, SZ3, Zfp, ZStd) and makes them usable from h5py.""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -31,4 +31,4 @@ modextrapaths = { 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', } -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb similarity index 96% rename from easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b rename to easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb index 05da9533301..5d5353e4024 100644 --- a/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b +++ b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb @@ -4,8 +4,8 @@ name = 'kundajelab-shap' version = '1' homepage = "https://github.com/kundajelab/shap" -description = """This is a custom fork of the shap repository that has support -for computing hypothetical importance scores, for use with TF-MoDISco. +description = """This is a custom fork of the shap repository that has support +for computing hypothetical importance scores, for use with TF-MoDISco. It was originally forked under AvantiShri/shap.""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -46,4 +46,4 @@ exts_list = [ }), ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb similarity index 92% rename from easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b rename to easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb index 5b30245e373..1c042f77b50 100644 --- a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b +++ b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb @@ -13,20 +13,20 @@ description = """TF-MoDISco is a motif detection algorithm that takes in nucleot toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('h5py', '3.6.0'), + ('h5py', '3.6.0'), ('hdf5plugin', '3.2.0'), - ('igraph', '0.9.5'), - ('python-igraph', '0.9.8'), + ('igraph', '0.9.5'), + ('python-igraph', '0.9.8'), ('leidenalg', '0.8.8'), ('matplotlib', '3.4.3'), ('numba', '0.54.1'), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.2'), ('tqdm', '4.62.3'), ] -use_pip = True +use_pip = True # Loosen unnecessarily strict version dependencies local_preinstallopts = "sed -i 's|numpy >= 1.21.5|numpy >= 1.21.3|g' setup.py && " @@ -57,6 +57,6 @@ sanity_check_commands = [ "modisco -h", "modisco motifs -h", "modisco report -h", -] +] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb similarity index 96% rename from easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b rename to easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb index c4169295732..8482a742518 100644 --- a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b +++ b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb @@ -11,18 +11,18 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('h5py', '3.6.0'), ('igraph', '0.9.5'), - ('leidenalg', '0.8.8'), + ('leidenalg', '0.8.8'), ('matplotlib', '3.4.3'), ('numba', '0.54.1'), # for pynndescent ('psutil', '5.9.4'), ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 + ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 ('scikit-learn', '1.0.2'), ('tqdm', '4.62.3'), ('TensorFlow', '2.8.4'), ] -use_pip = True +use_pip = True exts_list = [ ('joblib', '1.0.1', { @@ -52,6 +52,6 @@ sanity_check_commands = [ # enable write permissions, since installation directory may be read-only "mkdir -p %(builddir)s && cp -a %(installdir)s/test %(builddir)s/ && chmod -R u+wx %(builddir)s/test", "cd %(builddir)s/test && python test_core.py && python test_tfmodisco_workflow.py", -] +] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb index 0f868319ebf..b4a5dbab101 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.2.0.eb @@ -33,4 +33,4 @@ options = {'modulename': 'nose'} sanity_check_commands = ["nosetests --help"] -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb deleted file mode 100644 index 996aeca133c..00000000000 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'SlamDunk' -version = '0.4.3' - -homepage = 'https://t-neumann.github.io/slamdunk' -description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible -SLAMseq data analysis.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'] - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('pybedtools', '0.8.2'), - ('Pysam', '0.17.0'), - ('Biopython', '1.79'), - ('SAMtools', '1.14'), - ('VarScan', '2.4.4', '-Java-11', SYSTEM), - ('R', '4.1.2'), - ('NextGenMap', '0.5.5'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/slamdunk'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -sanity_check_commands = ["slamdunk --help"] - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb index 6ac146e203c..b1993fb8d2c 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-54.2.0-GCCcore-11.2.0.eb @@ -23,4 +23,4 @@ download_dep_fail = True sanity_pip_check = True use_pip = True -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b deleted file mode 100644 index c7bc833518b..00000000000 --- a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b +++ /dev/null @@ -1,73 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'WeasyPrint' -version = '52.5' - -homepage = 'https://github.com/Kozea/WeasyPrint' -description = """WeasyPrint is a smart solution helping web developers to create -PDF documents. It turns simple HTML pages into gorgeous statistical reports, -invoices, tickets.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('cairo', '1.16.0'), - ('setuptools', '54.2.0'), - ('cffi', '1.14.5'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.8'), - ('Python', '3.9.6'), - ('Pillow', '8.3.2'), -] - -use_pip = True - -exts_list = [ - ('cssselect2', '0.4.1', { - 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], - }), - ('cairocffi', '1.2.0', { - 'modulename': 'cairocffi', - 'source_tmpl': 'cairocffi-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], - 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], - }), - ('CairoSVG', '2.5.1', { - 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], - }), - ('html5lib', '1.1', { - 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], - }), - ('tinycss2', '1.1.0', { - 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], - }), - ('pydyf', '0.0.2', { - 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], - }), - ('pyphen', '0.10.0', { - 'modulename': 'pyphen', - 'source_tmpl': 'Pyphen-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], - 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], - }), - ('fonttools', '4.34.0', { - 'modulename': 'fontTools', - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], - }), - (name, version, { - 'modulename': 'weasyprint', - 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], - }), -] - -sanity_check_paths = { - 'files': ['bin/weasyprint'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["weasyprint --help"] - -sanity_pip_check = True - -moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb deleted file mode 100644 index c7bc833518b..00000000000 --- a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.2-foss-2021b.eb +++ /dev/null @@ -1,73 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'WeasyPrint' -version = '52.5' - -homepage = 'https://github.com/Kozea/WeasyPrint' -description = """WeasyPrint is a smart solution helping web developers to create -PDF documents. It turns simple HTML pages into gorgeous statistical reports, -invoices, tickets.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('cairo', '1.16.0'), - ('setuptools', '54.2.0'), - ('cffi', '1.14.5'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.8'), - ('Python', '3.9.6'), - ('Pillow', '8.3.2'), -] - -use_pip = True - -exts_list = [ - ('cssselect2', '0.4.1', { - 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], - }), - ('cairocffi', '1.2.0', { - 'modulename': 'cairocffi', - 'source_tmpl': 'cairocffi-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], - 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], - }), - ('CairoSVG', '2.5.1', { - 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], - }), - ('html5lib', '1.1', { - 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], - }), - ('tinycss2', '1.1.0', { - 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], - }), - ('pydyf', '0.0.2', { - 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], - }), - ('pyphen', '0.10.0', { - 'modulename': 'pyphen', - 'source_tmpl': 'Pyphen-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], - 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], - }), - ('fonttools', '4.34.0', { - 'modulename': 'fontTools', - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], - }), - (name, version, { - 'modulename': 'weasyprint', - 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], - }), -] - -sanity_check_paths = { - 'files': ['bin/weasyprint'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["weasyprint --help"] - -sanity_pip_check = True - -moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb index c7bc833518b..a0b0265f181 100644 --- a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb +++ b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb @@ -4,35 +4,35 @@ name = 'WeasyPrint' version = '52.5' homepage = 'https://github.com/Kozea/WeasyPrint' -description = """WeasyPrint is a smart solution helping web developers to create -PDF documents. It turns simple HTML pages into gorgeous statistical reports, +description = """WeasyPrint is a smart solution helping web developers to create +PDF documents. It turns simple HTML pages into gorgeous statistical reports, invoices, tickets.""" toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('cairo', '1.16.0'), - ('setuptools', '54.2.0'), - ('cffi', '1.14.5'), - ('Gdk-Pixbuf', '2.42.6'), + ('cairo', '1.16.0'), + ('setuptools', '54.2.0'), + ('cffi', '1.14.5'), + ('Gdk-Pixbuf', '2.42.6'), ('Pango', '1.48.8'), ('Python', '3.9.6'), ('Pillow', '8.3.2'), ] -use_pip = True +use_pip = True exts_list = [ ('cssselect2', '0.4.1', { 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], }), ('cairocffi', '1.2.0', { - 'modulename': 'cairocffi', + 'modulename': 'cairocffi', 'source_tmpl': 'cairocffi-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], - 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], - }), - ('CairoSVG', '2.5.1', { + 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], + }), + ('CairoSVG', '2.5.1', { 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], }), ('html5lib', '1.1', { @@ -44,19 +44,19 @@ exts_list = [ ('pydyf', '0.0.2', { 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], }), - ('pyphen', '0.10.0', { - 'modulename': 'pyphen', + ('pyphen', '0.10.0', { + 'modulename': 'pyphen', 'source_tmpl': 'Pyphen-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/P/Pyphen'], - 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], - }), + 'checksums': ['719b21dfb4b04fbc11cc0f6112418535fe35474021120cccfffc43a25fe63128'], + }), ('fonttools', '4.34.0', { 'modulename': 'fontTools', 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], - }), + }), (name, version, { - 'modulename': 'weasyprint', + 'modulename': 'weasyprint', 'checksums': ['b37ea02d75ca04babd7becad7341426be332ae560d8f02d664bfa1e9afb18481'], }), ] @@ -70,4 +70,4 @@ sanity_check_commands = ["weasyprint --help"] sanity_pip_check = True -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb index 89bbf23d8a0..74af84c4d84 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.6.1-foss-2021b.eb @@ -26,4 +26,4 @@ sanity_pip_check = True # use the parallel parameter from EB instead of total procs in the system preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' From e8031cb02d36fb42f76f8bd3c4d3be205730e089 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 12:00:52 +0200 Subject: [PATCH 06/25] Few extra format editions --- easybuild/easyconfigs/c/chrombpnet/.DS_Store | Bin 0 -> 6148 bytes easybuild/easyconfigs/m/modisco-lite/.DS_Store | Bin 0 -> 6148 bytes easybuild/easyconfigs/m/modisco/.DS_Store | Bin 0 -> 6148 bytes 3 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/c/chrombpnet/.DS_Store create mode 100644 easybuild/easyconfigs/m/modisco-lite/.DS_Store create mode 100644 easybuild/easyconfigs/m/modisco/.DS_Store diff --git a/easybuild/easyconfigs/c/chrombpnet/.DS_Store b/easybuild/easyconfigs/c/chrombpnet/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 Date: Fri, 31 May 2024 12:04:05 +0200 Subject: [PATCH 07/25] Remove .DS_Store files from tracking --- easybuild/easyconfigs/c/chrombpnet/.DS_Store | Bin 6148 -> 0 bytes easybuild/easyconfigs/m/modisco-lite/.DS_Store | Bin 6148 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 easybuild/easyconfigs/c/chrombpnet/.DS_Store delete mode 100644 easybuild/easyconfigs/m/modisco-lite/.DS_Store diff --git a/easybuild/easyconfigs/c/chrombpnet/.DS_Store b/easybuild/easyconfigs/c/chrombpnet/.DS_Store deleted file mode 100644 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 Date: Fri, 31 May 2024 12:04:26 +0200 Subject: [PATCH 08/25] Remove .DS_Store files from tracking --- easybuild/easyconfigs/m/modisco/.DS_Store | Bin 6148 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 easybuild/easyconfigs/m/modisco/.DS_Store diff --git a/easybuild/easyconfigs/m/modisco/.DS_Store b/easybuild/easyconfigs/m/modisco/.DS_Store deleted file mode 100644 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 Date: Fri, 31 May 2024 12:10:52 +0200 Subject: [PATCH 09/25] Few extra format editions --- .../c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb | 10 ++++++---- .../m/modisco-lite/modisco-lite-foss-2021b.eb | 2 +- .../m/modisco/modisco-0.5.16.0-foss-2021b.eb | 4 ++-- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb index 7aa658e4dc7..c08cff4a338 100644 --- a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb @@ -4,7 +4,9 @@ name = 'chrombpnet' version = '0.1.7' homepage = 'https://github.com/kundajelab/chrombpnet' -description = """ ChromBPNet is a fully convolutional neural network that uses dilated convolutions with residual connections to enable large receptive fields with efficient parameterization. It also performs automatic assay bias correction. """ +description = """ ChromBPNet is a fully convolutional neural network that uses dilated convolutions with residual +connections to enable large receptive fields with efficient parameterization. +It also performs automatic assay bias correction. """ toolchain = {'name': 'foss', 'version': '2021b'} @@ -27,7 +29,7 @@ dependencies = [ ('protobuf-python', '3.17.3'), ('tqdm', '4.62.3'), ('kundajelab-shap', '1'), - ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 + ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 ('WeasyPrint', '52.5'), ] @@ -43,14 +45,14 @@ local_preinstallopts += "sed -i 's|tqdm==|tqdm>=|g' requirements.txt && " local_preinstallopts += "sed -i 's|numpy== 1.23.4|numpy>=1.21.0|g' requirements.txt && " exts_list = [ - ( 'matplotlib-venn', '0.11.6', { + ('matplotlib-venn', '0.11.6', { 'checksums': ['d209a9845bb3a54c4247f1ef3f745e4819660ecc9208137097d2a51281f2a478'], }), ('tensorflow-estimator', '2.8.0', { 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], }), - ( 'deeplift', '0.6.13.0', { + ('deeplift', '0.6.13.0', { 'checksums': ['354ac5a00630b2df0856e8c948262e38c7eb83a719f71d6b5bf8ec4b064cb432'], }), (name, version, { diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb index 1c042f77b50..8746b418079 100644 --- a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb +++ b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb @@ -21,7 +21,7 @@ dependencies = [ ('matplotlib', '3.4.3'), ('numba', '0.54.1'), ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 + ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 ('scikit-learn', '1.0.2'), ('tqdm', '4.62.3'), ] diff --git a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb index 8482a742518..beee99dab77 100644 --- a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb @@ -13,10 +13,10 @@ dependencies = [ ('igraph', '0.9.5'), ('leidenalg', '0.8.8'), ('matplotlib', '3.4.3'), - ('numba', '0.54.1'), # for pynndescent + ('numba', '0.54.1'), # for pynndescent ('psutil', '5.9.4'), ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 + ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 ('scikit-learn', '1.0.2'), ('tqdm', '4.62.3'), ('TensorFlow', '2.8.4'), From 290d576b47895b41644da97fae4981ad82597d43 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 12:29:42 +0200 Subject: [PATCH 10/25] Fix missing version of modico-lite in the easyconfig name --- .../modisco-lite-2.0.7-foss-2021b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb new file mode 100644 index 00000000000..8746b418079 --- /dev/null +++ b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'modisco-lite' +version = '2.0.7' + +homepage = 'https://github.com/jmschrei/tfmodisco-lite' +description = """TF-MoDISco is a motif detection algorithm that takes in nucleotide + sequence and the attributions from a neural network model and return motifs + that are repeatedly enriched for attriution score across the examples. + This tool will take in one-hot encoded sequence, the corresponding + attribution scores, and a few other parameters, and return the motifs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('h5py', '3.6.0'), + ('hdf5plugin', '3.2.0'), + ('igraph', '0.9.5'), + ('python-igraph', '0.9.8'), + ('leidenalg', '0.8.8'), + ('matplotlib', '3.4.3'), + ('numba', '0.54.1'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 + ('scikit-learn', '1.0.2'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +# Loosen unnecessarily strict version dependencies +local_preinstallopts = "sed -i 's|numpy >= 1.21.5|numpy >= 1.21.3|g' setup.py && " +local_preinstallopts += "sed -i 's|pandas >= 1.4.3|pandas >= 1.3.4|g' setup.py && " +local_preinstallopts += "sed -i 's|leidenalg == 0.8.10|leidenalg >= 0.8.8|g' setup.py && " +local_preinstallopts += "sed -i 's|igraph == 0.9.11|igraph >= 0.9.5|g' setup.py && " +local_preinstallopts += "sed -i 's|h5py >= 3.7.0|h5py >= 3.6.0|g' setup.py && " + +exts_list = [ + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + (name, version, { + 'modulename': 'modiscolite', + 'preinstallopts': local_preinstallopts, + 'checksums': ['937a570cd0b5cff67daddb05215f5ee4820b2f67bf8bb0e2088424a217953eef'], + }), +] + +sanity_check_paths = { + 'files': ['bin/modisco'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +sanity_check_commands = [ + "modisco -h", + "modisco motifs -h", + "modisco report -h", +] + +moduleclass = 'bio' From 23d9dafa5bcae9c6ca9fe6be99e8f32be722e02f Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 13:06:37 +0200 Subject: [PATCH 11/25] Remove modisco-lite-foss-2021b.eb missing version --- .../m/modisco-lite/modisco-lite-foss-2021b.eb | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb deleted file mode 100644 index 8746b418079..00000000000 --- a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-foss-2021b.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'modisco-lite' -version = '2.0.7' - -homepage = 'https://github.com/jmschrei/tfmodisco-lite' -description = """TF-MoDISco is a motif detection algorithm that takes in nucleotide - sequence and the attributions from a neural network model and return motifs - that are repeatedly enriched for attriution score across the examples. - This tool will take in one-hot encoded sequence, the corresponding - attribution scores, and a few other parameters, and return the motifs.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('h5py', '3.6.0'), - ('hdf5plugin', '3.2.0'), - ('igraph', '0.9.5'), - ('python-igraph', '0.9.8'), - ('leidenalg', '0.8.8'), - ('matplotlib', '3.4.3'), - ('numba', '0.54.1'), - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 - ('scikit-learn', '1.0.2'), - ('tqdm', '4.62.3'), -] - -use_pip = True - -# Loosen unnecessarily strict version dependencies -local_preinstallopts = "sed -i 's|numpy >= 1.21.5|numpy >= 1.21.3|g' setup.py && " -local_preinstallopts += "sed -i 's|pandas >= 1.4.3|pandas >= 1.3.4|g' setup.py && " -local_preinstallopts += "sed -i 's|leidenalg == 0.8.10|leidenalg >= 0.8.8|g' setup.py && " -local_preinstallopts += "sed -i 's|igraph == 0.9.11|igraph >= 0.9.5|g' setup.py && " -local_preinstallopts += "sed -i 's|h5py >= 3.7.0|h5py >= 3.6.0|g' setup.py && " - -exts_list = [ - ('logomaker', '0.8', { - 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], - }), - (name, version, { - 'modulename': 'modiscolite', - 'preinstallopts': local_preinstallopts, - 'checksums': ['937a570cd0b5cff67daddb05215f5ee4820b2f67bf8bb0e2088424a217953eef'], - }), -] - -sanity_check_paths = { - 'files': ['bin/modisco'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_pip_check = True - -sanity_check_commands = [ - "modisco -h", - "modisco motifs -h", - "modisco report -h", -] - -moduleclass = 'bio' From 4b3e27791c34bef1fd61bfbd2f22ca7a085ba00f Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 13:32:11 +0200 Subject: [PATCH 12/25] adding back a locally missing eb --- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb new file mode 100644 index 00000000000..996aeca133c --- /dev/null +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'SlamDunk' +version = '0.4.3' + +homepage = 'https://t-neumann.github.io/slamdunk' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible +SLAMseq data analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('pybedtools', '0.8.2'), + ('Pysam', '0.17.0'), + ('Biopython', '1.79'), + ('SAMtools', '1.14'), + ('VarScan', '2.4.4', '-Java-11', SYSTEM), + ('R', '4.1.2'), + ('NextGenMap', '0.5.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/slamdunk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["slamdunk --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ec493a6e21d7fa134934602f7ee236e8993737ba Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 31 May 2024 14:26:09 +0200 Subject: [PATCH 13/25] fix a bug --- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb new file mode 100644 index 00000000000..9b485eb958a --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.2' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('Pillow', '8.3.2'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + (name, version, { + 'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' From 1bb5f90cc25e9dc473bddd33b6fc16dc51c70150 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Tue, 4 Jun 2024 11:06:22 +0200 Subject: [PATCH 14/25] Delete easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb Duplicated file --- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb deleted file mode 100644 index 9b485eb958a..00000000000 --- a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '2.4.2' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('PyYAML', '5.4.1'), - ('Pillow', '8.3.2'), - ('SciPy-bundle', '2021.10'), -] - -use_pip = True - -exts_list = [ - ('tornado', '6.2', { - 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], - }), - (name, version, { - 'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'], - }), -] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["bokeh --help"] - -moduleclass = 'tools' From f72cb21171bf198eebebe93a2131f3c43d25b2e5 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Sat, 8 Jun 2024 10:17:49 +0200 Subject: [PATCH 15/25] Small fix in chrombpnet and WeasyPrint easyconfigs --- .../c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb | 2 +- .../w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb index c08cff4a338..5d648488f4f 100644 --- a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb @@ -42,7 +42,7 @@ local_preinstallopts += "sed -i 's|tensorflow==|tensorflow>=|g' requirements.txt local_preinstallopts += "sed -i 's|tensorflow-probability==|tensorflow-probability>=|g' requirements.txt && " local_preinstallopts += "sed -i 's|protobuf==3.20|protobuf>=3.17.0|g' requirements.txt && " local_preinstallopts += "sed -i 's|tqdm==|tqdm>=|g' requirements.txt && " -local_preinstallopts += "sed -i 's|numpy== 1.23.4|numpy>=1.21.0|g' requirements.txt && " +local_preinstallopts += "sed -i 's|numpy==1.23.4|numpy>=1.21.0|g' requirements.txt && " exts_list = [ ('matplotlib-venn', '0.11.6', { diff --git a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb index a0b0265f181..74efe666fe5 100644 --- a/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb +++ b/easybuild/easyconfigs/w/WeasyPrint/WeasyPrint-52.5-foss-2021b.eb @@ -23,6 +23,9 @@ dependencies = [ use_pip = True exts_list = [ + ('tinycss2', '1.1.0', { + 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], + }), ('cssselect2', '0.4.1', { 'checksums': ['93fbb9af860e95dd40bf18c3b2b6ed99189a07c0f29ba76f9c5be71344664ec8'], }), @@ -32,15 +35,15 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cairocffi'], 'checksums': ['9a979b500c64c8179fec286f337e8fe644eca2f2cd05860ce0b62d25f22ea140'], }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), ('CairoSVG', '2.5.1', { 'checksums': ['bfa0deea7fa0b9b2f29e41b747a915c249dbca731a4667c2917e47ff96e773e0'], }), ('html5lib', '1.1', { 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), - ('tinycss2', '1.1.0', { - 'checksums': ['fbdcac3044d60eb85fdb2aa840ece43cf7dbe798e373e6ee0be545d4d134e18a'], - }), ('pydyf', '0.0.2', { 'checksums': ['7c7f417413877edfc882f200834ee2415aa21c8cbfbc87802d78e12334a16581'], }), From 46420e4631609a2eca8a85c53b361e13b38a0adb Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:28:19 +0200 Subject: [PATCH 16/25] Delete easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb It is causing test building error "Found 2 variants of 'SAMtools' dependency in easyconfigs using '2021b' toolchain generation" --- .../s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb deleted file mode 100644 index a1a0f8bdecf..00000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT -# -# Notes:: -# -# Updated to 1.14 and gcc-11.2.0 -# J. Sassmannshausen / GSTT - -name = 'SAMtools' -version = '1.14' - -homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74'] - -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.5'), - ('cURL', '7.78.0'), -] - -moduleclass = 'bio' From 454af6cb251a28c7799732b2ab81d197032c2b7c Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:29:54 +0200 Subject: [PATCH 17/25] Delete easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb It is causing test building error: "Found 2 variants of 'TensorFlow' dependency in easyconfigs using '2021b' toolchain generation" --- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 244 ------------------ 1 file changed, 244 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb deleted file mode 100644 index 7662b34846b..00000000000 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ /dev/null @@ -1,244 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'TensorFlow' -version = '2.7.1' - -homepage = 'https://www.tensorflow.org/' -description = "An open-source software library for Machine Intelligence" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'pic': True} - -builddependencies = [ - ('Bazel', '3.7.2'), - ('protobuf', '3.17.3'), - # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 - ('git', '2.33.1', '-nodocs'), - ('pybind11', '2.7.1'), - ('UnZip', '6.0'), -] -dependencies = [ - ('Python', '3.9.6'), - ('h5py', '3.6.0'), - ('cURL', '7.78.0'), - ('double-conversion', '3.1.5'), - ('flatbuffers', '2.0.0'), - ('giflib', '5.2.1'), - ('hwloc', '2.5.0'), - ('ICU', '69.1'), - ('JsonCpp', '1.9.4'), - ('libjpeg-turbo', '2.0.6'), - ('LMDB', '0.9.29'), - ('NASM', '2.15.05'), - ('nsync', '1.24.0'), - ('SQLite', '3.36'), - ('protobuf-python', '3.17.3'), - ('flatbuffers-python', '2.0'), - ('libpng', '1.6.37'), - ('snappy', '1.1.9'), - ('zlib', '1.2.11'), - ('networkx', '2.6.3'), # required for pythran -] - -use_pip = True -sanity_pip_check = True - -# Dependencies created and updated using findPythonDeps.sh: -# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d -exts_list = [ - # gast deps beniget and pythran require different version from Scipy-bundle - ('beniget', '0.3.0', { - 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], - }), - ('pythran', '0.9.11', { - 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], - }), - ('wrapt', '1.13.3', { - 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('tensorflow_estimator', '2.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['325b5a224864379242b7b76c6987ca544239be82579d33e68ec7c2bda57abc9d'], - }), - ('Werkzeug', '2.0.3', { - 'checksums': ['b863f8ff057c522164b6067c9e28b041161b4be5ba4d0daceeaa50a163822d3c'], - }), - ('tensorboard_plugin_wit', '1.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], - }), - ('tensorboard_data_server', '0.6.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], - }), - ('Markdown', '3.3.6', { - 'checksums': ['76df8ae32294ec39dcf89340382882dfa12975f87f45c3ed1ecdb1e8cefc7006'], - }), - ('grpcio', '1.43.0', { - 'modulename': 'grpc', - 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", - 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], - }), - ('oauthlib', '3.2.0', { - 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], - }), - ('requests-oauthlib', '1.3.1', { - 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], - }), - ('rsa', '4.8', { - 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], - }), - ('pyasn1-modules', '0.2.8', { - 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], - }), - ('cachetools', '5.0.0', { - 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], - }), - ('google-auth', '2.6.0', { - 'modulename': 'google.auth', - 'checksums': ['ad160fc1ea8f19e331a16a14a79f3d643d813a69534ba9611d2c80dc10439dad'], - }), - ('google-auth-oauthlib', '0.4.6', { - 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], - }), - ('tensorboard', '2.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], - }), - ('opt_einsum', '3.3.0', { - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - ('Keras_Preprocessing', '1.1.2', { - 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], - }), - ('keras', '2.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['0c33ae1f728064ca0d35dfba999e9c316f03623bf5688c82fb83cc74a80ea248'], - }), - ('google-pasta', '0.2.0', { - 'modulename': 'pasta', - 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], - }), - ('gast', '0.4.0', { - 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], - }), - ('astunparse', '1.6.3', { - 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], - }), - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard_plugin_profile', '2.5.0', { - 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], - }), - ('astor', '0.8.1', { - 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], - }), - ('dill', '0.3.4', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], - }), - ('tblib', '1.7.0', { - 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], - }), - ('portpicker', '1.5.0', { - 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], - }), - ('absl-py', '0.13.0', { - 'modulename': 'absl', - 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'patches': [ - 'TensorFlow-2.1.0_fix-cuda-build.patch', - 'TensorFlow-2.4.0_add-ldl.patch', - 'TensorFlow-2.4.0_dont-use-var-lock.patch', - 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', - 'TensorFlow-2.5.0_disable-avx512-extensions.patch', - 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', - 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', - 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', - 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', - 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', - 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', - 'TensorFlow-2.7.1_remove-libclang-dependency.patch', - 'TensorFlow-2.7.1_fix_cpu_count.patch', - 'TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch', - 'TensorFlow-2.7.1_fix-PPC-JIT.patch', - ], - 'checksums': [ - 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.5.0_add-support-for-large-core-systems.patch - '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', - # TensorFlow-2.5.0_disable-avx512-extensions.patch - '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', - # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch - '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', - # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', - # TensorFlow-2.5.0_fix-crash-on-shutdown.patch - '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', - # TensorFlow-2.7.1_fix_protobuf_error_message.patch - '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', - # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch - 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', - # TensorFlow-2.7.1_remove-io-gcs-dependency.patch - '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', - # TensorFlow-2.7.1_remove-libclang-dependency.patc - 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', - # TensorFlow-2.7.1_fix_cpu_count.patch - '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', - # TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch - 'ab647e80af52950c733d084ef9ec4b49780ab20a413476374cf41e25bd20af83', - # TensorFlow-2.7.1_fix-PPC-JIT.patch - 'f0652557e760fdc2b39313a24d6236e7c3984cabc3353e0d867e275ff90a13fe', - ], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' - '-benchmark-test,-v1only'), - 'test_targets': [ - '//tensorflow/core/...', - '-//tensorflow/core:example_java_proto', - '-//tensorflow/core/example:example_protos_closure', - '//tensorflow/cc/...', - '//tensorflow/c/...', - '//tensorflow/python/...', - # Fails on some nodes but C API isn't installed anyway - '-//tensorflow/c/eager:c_api_test_gpu', - '-//tensorflow/c/eager:c_api_distributed_test', - '-//tensorflow/c/eager:c_api_distributed_test_gpu', - # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 - '-//tensorflow/c/eager:c_api_cluster_test_gpu', - '-//tensorflow/c/eager:c_api_remote_function_test_gpu', - '-//tensorflow/c/eager:c_api_remote_test_gpu', - # Fails to open its own test.xml(?) - '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', - # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 - '-//tensorflow/core/common_runtime:mkl_layout_pass_test', - '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', - # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 - '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', - # All tests in this directory fail with segfault (TensorFlow Graph IR) - '-//tensorflow/core/ir/importexport/tests/roundtrip/...', - # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 - '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', - ], - 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + - "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", - 'with_xla': True, - }), -] - -moduleclass = 'lib' From cc65d27b939a0a6c40fd1fa87f4b351ac10e16e0 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:31:48 +0200 Subject: [PATCH 18/25] Delete easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb It is causing test building error "Found 3 variants of 'scikit-learn' dependency in easyconfigs using '2021b' toolchain generation" --- .../scikit-learn-1.0.1-foss-2021b.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb deleted file mode 100644 index d3f7980867c..00000000000 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '1.0.1' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10') -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'checksums': ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'], - 'modulename': 'sklearn', - }), - ('sklearn', '0.0', { # also install the meta-package, as other packages check for this - 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], - }) -] - -moduleclass = 'data' From 53ecc8006a830618be88b9a6e89b82ca278a8c14 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 13 Jun 2024 09:32:50 +0200 Subject: [PATCH 19/25] Delete easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb It is causing test building error "Found 3 variants of 'scikit-learn' dependency in easyconfigs using '2021b' toolchain generation" --- ...t-learn-0.20.4-foss-2021b-Python-2.7.18.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb deleted file mode 100644 index 2e978bde2c2..00000000000 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '0.20.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2021.10', versionsuffix) -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'patches': ['scikit-learn-0.20.3_fix-cd_fast.patch'], - 'checksums': [ - {'scikit-learn-0.20.4.tar.gz': 'dfa8a3f33907614030cdfbc8b6f553dacbecaf09f922244f128af3060a137cfc'}, - {'scikit-learn-0.20.3_fix-cd_fast.patch': - '9a98785a99bde000a58048ccbe382ea362aa8cf644171097e8ae755cddddeb75'}, - ], - 'modulename': 'sklearn', - }), - ('sklearn', '0.0', { - 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], - }), -] - -moduleclass = 'data' From 20f72808a4cac7594715a4d65348cab1867546d9 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 13 Jun 2024 15:28:43 +0200 Subject: [PATCH 20/25] fix duplicated variants of SAMtools using foss-2021b --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb | 2 +- easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb | 2 +- easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb | 2 +- .../easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb | 2 +- easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb | 2 +- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 2 +- easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb | 4 ++-- easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb | 2 +- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 2 +- ...Dunk-0.4.3-foss-2021b.eb => SlamDunk-0.4.3-foss-2021b.eb} | 2 +- .../easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb | 2 +- .../easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb | 2 +- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb | 2 +- 16 files changed, 17 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/s/SlamDunk/{SlamDunk-0.4.3-foss-2021b.eb => SlamDunk-0.4.3-foss-2021b.eb} (97%) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb index 2c6961e4449..3787f6343a7 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb @@ -29,7 +29,7 @@ dependencies = [ ('zlib', '1.2.11'), ('Boost', '1.77.0'), ('GSL', '2.7'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('HTSlib', '1.14'), # also provides tabix ('BCFtools', '1.14'), ('lpsolve', '5.5.2.11'), diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb index a1aa7296bbc..f15c3248c7f 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('AUGUSTUS', '3.4.0'), ('GeneMark-ET', '4.71'), ('BamTools', '2.5.2'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), ('spaln', '2.4.12'), ('Exonerate', '2.4.0'), diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb index 1034b4e9a44..8a5a390200a 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb @@ -25,7 +25,7 @@ checksums = ['2ceb620cfc3f1c869f4bda656ab01c242f1da7ec01615b0d23b28c702147a337'] dependencies = [ ('Perl', '5.34.0'), ('Bowtie2', '2.4.4'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ] sanity_check_commands = ['bismark --help'] diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb index 98ab2c0bfa1..1391dda1a7d 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb @@ -18,7 +18,7 @@ checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'] builddependencies = [ ('Eigen', '3.3.9'), ('Autotools', '20210726'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('Boost', '1.75.0'), ] diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb index 64d414e98e3..9e0c9d302c7 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb @@ -21,7 +21,7 @@ dependencies = [ ('snakemake', '6.10.0'), ('wget', '1.21.2'), ('HTSlib', '1.14'), # for tabix - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('BCFtools', '1.14'), ('Pandoc', '2.13', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb index 8cf70e725c4..df36a988582 100644 --- a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb @@ -26,7 +26,7 @@ checksums = [ dependencies = [ ('STAR', '2.7.9a'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('BEDTools', '2.30.0'), ('AUGUSTUS', '3.4.0'), ('BRAKER', '2.1.6'), diff --git a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb index 68924b5d99d..3ad9d4bd77b 100644 --- a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb +++ b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb @@ -31,7 +31,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('picard', '2.25.1', versionsuffix, SYSTEM), ('R', '4.1.2'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb index 90f8eac533d..103bd982a60 100644 --- a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb @@ -18,7 +18,7 @@ dependencies = [ ('Java', '15', '', SYSTEM), ('minimap2', '2.22'), ('HTSlib', '1.14'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('Racon', '1.5.0'), ] diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 3ffd2f88277..02179b2ebd8 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -31,7 +31,7 @@ dependencies = [ ('Perl', '5.34.0'), ('Boost', '1.77.0'), ('zlib', '1.2.11'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), ] diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb index f13a44b0e6e..6a55f7a270d 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb @@ -24,9 +24,9 @@ _minimap_ver = '2.22' dependencies = [ ('Python', '3.9.6'), # includes cffi # TensorFlow ~=2.7.0 required by medaka 1.6.0, see requirements.txt - ('TensorFlow', '2.7.1'), + ('TensorFlow', '2.8.4'), ('Pysam', '0.18.0'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('minimap2', _minimap_ver), ('HTSlib', '1.14'), # for tabix, bgzip ('Racon', '1.5.0'), diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index ffeef5eccb8..26b3a43d326 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -18,7 +18,7 @@ dependencies = [ ('cutadapt', '3.5'), ('Bowtie2', '2.4.4'), ('Bowtie', '1.3.1'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('picard', '2.25.1', '-Java-11', SYSTEM), ('GSL', '2.7'), ('Kent_tools', '422'), diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index 841410ab2b3..275c82085cd 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -17,7 +17,7 @@ checksums = ['b31263b64aefe97bdc4d7fae138f515a7d7a60cd05031d38dd89a10f9ee10cd1'] dependencies = [ ('R', '4.1.2'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), ] diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb similarity index 97% rename from easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb rename to easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 996aeca133c..60595bd52ec 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -18,7 +18,7 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Pysam', '0.17.0'), ('Biopython', '1.79'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('VarScan', '2.4.4', '-Java-11', SYSTEM), ('R', '4.1.2'), ('NextGenMap', '0.5.5'), diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb index f1a8cec6d8d..9cfaed62b17 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb @@ -45,7 +45,7 @@ dependencies = [ ('MUMmer', '4.0.0beta2'), ('pplacer', '1.1.alpha19', '', SYSTEM), ('Short-Pair', '20170125'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('CompareM', '0.1.2'), ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s') # provides pathview needed for SQMtools ] diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb index c9b055c0b96..3a911645982 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb @@ -20,7 +20,7 @@ dependencies = [ ('BWA', '0.7.17'), ('BCFtools', '1.14'), ('BEDTools', '2.30.0'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('parallel', '20210722'), ('minimap2', '2.22'), ('vt', '0.57721'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb index d904f619a21..c636c2d4d50 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb @@ -53,7 +53,7 @@ dependencies = [ ('ncurses', '6.2'), ('RSEM', '1.3.3'), ('Salmon', '1.4.0'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('STAR', '2.7.9a'), ('zlib', '1.2.11'), ] From 995eaaa14a093faad1edd67e628048eb25e3c05a Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 13 Jun 2024 15:39:42 +0200 Subject: [PATCH 21/25] fix duplicated variants of SAMtools using foss-2021b --- .../easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb | 2 +- .../g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb | 2 +- easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb index 18991c61de3..5f46eb192ea 100644 --- a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb @@ -44,7 +44,7 @@ dependencies = [ ('Proteinortho', '6.2.3'), ('Kent_tools', '422'), # provides pslCDnaFilter ('Salmon', '1.4.0'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('SignalP', '6.0g', '-fast'), ('SNAP', '2.0.1'), ('StringTie', '2.2.1'), diff --git a/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb index 1778ef1545b..8e635e7886f 100644 --- a/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb @@ -20,7 +20,7 @@ dependencies = [ ('KMC', '3.2.1', versionsuffix), ('Velvet', '1.2.10', '-mt-kmer_191'), ('BWA', '0.7.17'), - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('BamTools', '2.5.2'), ] diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb index 8c9d1678e1d..a8e66b107f7 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb @@ -15,7 +15,7 @@ checksums = ['b7323e6586238821202cf9644963e584e7397a5cee23e564d00b07fcb344ecd2'] # excluded (optional) dependency: skesa # cfr. https://github.com/ncbi/ngs-tools/tree/master/tools/skesa dependencies = [ - ('SAMtools', '1.14'), + ('SAMtools', '1.15.1'), ('BWA', '0.7.17'), ('Mash', '2.3'), ('seqtk', '1.3'), From 6802b9d8abb20713bdbde9d7a82975e196ac2b0d Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 13 Jun 2024 15:46:40 +0200 Subject: [PATCH 22/25] fix duplicated variants of TensorFlow using foss-2021b --- easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb index 52279474a01..e0b5f623680 100644 --- a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.6'), - ('TensorFlow', '2.7.1'), + ('TensorFlow', '2.8.4'), ('Abseil', '20210324.2'), ('dm-tree', '0.1.6'), ('gRPC', '1.44.0'), diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb index 527256b2790..ed2e5e41975 100644 --- a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True} dependencies = [ ('Python', '3.9.6'), - ('TensorFlow', '2.7.1'), + ('TensorFlow', '2.8.4'), ('numba', '0.54.1'), ('imageio', '2.13.5'), ('scikit-image', '0.19.1'), From 3336a2856a87de2d7afc3318a569159153fffa17 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 13 Jun 2024 16:03:08 +0200 Subject: [PATCH 23/25] fix duplicated variants of scikit-learn using foss-2021b --- .../chrombpnet/chrombpnet-0.1.7-foss-2021b.eb | 2 +- .../kundajelab-shap-1-foss-2021b.eb | 2 +- .../modisco-lite-2.0.7-foss-2021b.eb | 3 +- .../m/modisco/modisco-0.5.16.0-foss-2021b.eb | 2 +- .../scikit-learn-1.0.2-foss-2021b.eb | 32 ------------------- 5 files changed, 5 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb index 5d648488f4f..2a90eb4c863 100644 --- a/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/chrombpnet/chrombpnet-0.1.7-foss-2021b.eb @@ -23,7 +23,7 @@ dependencies = [ ('matplotlib', '3.4.3'), ('modisco', '0.5.16.0'), ('modisco-lite', '2.0.7'), - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.1'), ('TensorFlow', '2.8.4'), ('tensorflow-probability', '0.16.0'), ('protobuf-python', '3.17.3'), diff --git a/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb index 5d5353e4024..22cf97d899a 100644 --- a/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb +++ b/easybuild/easyconfigs/k/kundajelab-shap/kundajelab-shap-1-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('IPython', '7.26.0'), ('matplotlib', '3.4.3'), ('SciPy-bundle', '2021.10'), - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.1'), ('scikit-image', '0.19.1'), ('tqdm', '4.62.3'), ('numba', '0.54.1'), diff --git a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb index 8746b418079..8380cd05a04 100644 --- a/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb +++ b/easybuild/easyconfigs/m/modisco-lite/modisco-lite-2.0.7-foss-2021b.eb @@ -22,7 +22,7 @@ dependencies = [ ('numba', '0.54.1'), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), # for numpy=1.21.3, pandas=1.3.4 and scipy=1.7.1 - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.1'), ('tqdm', '4.62.3'), ] @@ -30,6 +30,7 @@ use_pip = True # Loosen unnecessarily strict version dependencies local_preinstallopts = "sed -i 's|numpy >= 1.21.5|numpy >= 1.21.3|g' setup.py && " +local_preinstallopts += "sed -i 's|scikit-learn >= 1.0.2|scikit-learn >= 1.0.0|g' setup.py && " local_preinstallopts += "sed -i 's|pandas >= 1.4.3|pandas >= 1.3.4|g' setup.py && " local_preinstallopts += "sed -i 's|leidenalg == 0.8.10|leidenalg >= 0.8.8|g' setup.py && " local_preinstallopts += "sed -i 's|igraph == 0.9.11|igraph >= 0.9.5|g' setup.py && " diff --git a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb index beee99dab77..e4870b27889 100644 --- a/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/modisco/modisco-0.5.16.0-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ ('psutil', '5.9.4'), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), # for numpy 1.21 and pandas 1.3.4 - ('scikit-learn', '1.0.2'), + ('scikit-learn', '1.0.1'), ('tqdm', '4.62.3'), ('TensorFlow', '2.8.4'), ] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb deleted file mode 100644 index 668090f02d8..00000000000 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'scikit-learn' -version = '1.0.2' - -homepage = 'https://scikit-learn.org/stable/index.html' -description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, -building upon numpy, scipy, and matplotlib. As a machine-learning module, -it provides versatile tools for data mining and analysis in any field of science and engineering. -It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10') -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'checksums': ['b5870959a5484b614f26d31ca4c17524b1b0317522199dc985c3b4256e030767'], - 'modulename': 'sklearn', - }), - ('sklearn', '0.0', { # also install the meta-package, as other packages check for this - 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], - }) -] - -moduleclass = 'data' From 78d134cb9f6d1f6e7095e88895c5aa89436ea94c Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 13 Jun 2024 16:33:14 +0200 Subject: [PATCH 24/25] fix issues with duplicated dependencies of scikit learn versions --- ...1.1.2-20221201-foss-2021b-Python-2.7.18.eb | 50 ------------------- .../scikit-learn-1.0.1-foss-2021b.eb | 33 ++++++++++++ 2 files changed, 33 insertions(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb deleted file mode 100644 index b2f6bd3849e..00000000000 --- a/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'CIRIquant' -local_commit = '2d0663e' -version = '1.1.2-20221201' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/bioinfo-biols/CIRIquant' -description = "CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '2.7.18'), - ('SciPy-bundle', '2021.10', versionsuffix), - ('PyYAML', '5.4.1', versionsuffix), - ('Pysam', '0.17.0', versionsuffix), - ('scikit-learn', '0.20.4', versionsuffix), -] - -use_pip = True - -exts_list = [ - ('argparse', '1.4.0', { - 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], - }), - (name, version, { - 'source_urls': ['https://github.com/bioinfo-biols/CIRIquant/archive/'], - 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], - 'checksums': ['4990122c0eb820b1ec9cfc64fcfe49d3f9680dae69719dba3f8a7d77f9c3ff54'], - # relax numpy version requirement, no actual need for 1.22.0 - # (cfr. https://github.com/bioinfo-biols/CIRIquant/pull/39), - # and remove very strict version requirements for all required Python packages - 'preinstallopts': "sed -i 's/numpy==1.22.0/numpy==1.16.4/g' setup.py && sed -i 's/==/>=/g' setup.py && ", - 'modulename': 'CIRIquant', - }), -] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/CIRIquant'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["CIRIquant --help"] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/CIRIquant'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb new file mode 100644 index 00000000000..e6532d73cde --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.0.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'], + 'modulename': 'sklearn', + }), + ('sklearn', '0.0', { # also install the meta-package, as other packages check for this + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }) +] + +moduleclass = 'data' + From 8b51082ccf0c6c311f7c64966fb3c8fe878f19e8 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 13 Jun 2024 18:54:18 +0200 Subject: [PATCH 25/25] Update scikit-learn-1.0.1-foss-2021b.eb --- .../easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb index e6532d73cde..d3f7980867c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb @@ -30,4 +30,3 @@ exts_list = [ ] moduleclass = 'data' -