diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb new file mode 100644 index 000000000000..6d8e9f256971 --- /dev/null +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Vamb' +version = '3.0.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/RasmussenLab/vamb' +description = """Vamb is a metagenomic binner which feeds sequence +composition information from a contig catalogue and co-abundance +information from BAM files into a variational autoencoder and clusters +the latent representation.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pysam', '0.17.0'), + ('PyTorch', '1.12.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools', '59.6.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_allow_pytorch_1.12.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RasmussenLab/vamb/archive'], + 'checksums': [ + {'v3.0.9.tar.gz': '3a9025ddc3e9e54e3debe65855ac2367335f920efbcb9e5ecc671a1036455d1e'}, + {'Vamb-3.0.9_allow_pytorch_1.12.patch': '52f909a91d7d63ead3dfa1314c66efb2918a3606212a8f3d8e3a9f7ee7b33c86'}, + ], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch new file mode 100644 index 000000000000..f19bf52595b7 --- /dev/null +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch @@ -0,0 +1,15 @@ +Drop requirement of pytorch to 1.12 to allow the use of foss/2021b toolchain + +Åke Sandgren, 2023-03-01 +diff -ru vamb-3.0.9.orig/setup.py vamb-3.0.9/setup.py +--- vamb-3.0.9.orig/setup.py 2022-11-24 11:02:48.000000000 +0100 ++++ vamb-3.0.9/setup.py 2023-03-01 08:26:12.432734868 +0100 +@@ -22,7 +22,7 @@ + "ext_modules": [Extension("vamb._vambtools", + sources=["src/_vambtools.pyx"], + language="c")], +- "install_requires": ["numpy>=1.20", "torch>=1.13", "pysam>=0.14"], ++ "install_requires": ["numpy>=1.20", "torch>=1.12", "pysam>=0.14"], + "setup_requires": ['Cython>=0.29', "setuptools>=58.0"], + "python_requires": ">=3.5", + "classifiers":[