diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..83cbc16113e --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.8.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.8.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('PyTorch', '2.1.2', versionsuffix), + ('edlib', '1.3.9'), + ('ont-fast5-api', '4.1.2'), + ('ont-remora', '3.3.0', versionsuffix), + ('python-parasail', '1.3.4'), + ('pod5-file-format', '0.3.10'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('fast-ctc-decode', '0.3.6', { + 'source_tmpl': 'fast_ctc_decode-0.3.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['f49994a475866edf0e61f0d9e1b41185c035ba559b8c2aa68f83342d2c80ee6b'], + }), + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + ('ont_koi', '0.4.4', { + 'source_tmpl': 'ont_koi-0.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'modulename': 'koi', + 'checksums': ['e5d7c93b26363a3d4e3778f972d1f149447adbde91925e8876a97e7a63774e28'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'checksums': ['26df86ee233bf020b549177e1e2aaa7ad7d99cf0927d79ab3fa31c1670d09ba6'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3fcee4f2eb2 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-3.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '3.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('python-parasail', '1.3.4'), + ('polars', '0.20.2'), + ('Pysam', '0.22.0'), + ('pod5-file-format', '0.3.10'), + ('statsmodels', '0.14.1'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.1.1.post2209072238', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'], + }), + ('mizani', '0.9.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ac5d49b913de88dc2fb28d82141e9777b97407a6971a158f758093ad5bb820a1'], + }), + ('plotnine', '0.12.4', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['12748f346f107c33f3e0658ac46fbb052205ae7e97ffaf52be68310e5d29f799'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['3c899e7333ae33ebec31c8a59650ab4d553e8a62c0abf7b03899e2ee9a0bc88a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio'