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Merge pull request #18651 from boegel/20230825180542_new_pr_medaka191
{bio}[foss/2022a] medaka v1.9.1
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# This is a contribution from HPCNow! (http://hpcnow.com) | ||
# Copyright:: HPCNow! | ||
# Authors:: Danilo Gonzalez <danilo.gonzalez@hpcnow.com> | ||
# License:: GPL-v3.0 | ||
# Updated to foss-2020b to use with artic tool | ||
# J. Sassmannshausen (GSTT/NHS UK) | ||
# Updated to 1.5.0 | ||
# Jasper Grimm (UoY) | ||
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easyblock = 'PythonBundle' | ||
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name = 'medaka' | ||
version = '1.9.1' | ||
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homepage = 'https://github.com/nanoporetech/medaka' | ||
description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." | ||
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toolchain = {'name': 'foss', 'version': '2022a'} | ||
toolchainopts = {'pic': True} | ||
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builddependencies = [('Autotools', '20220317')] | ||
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_minimap_ver = '2.24' | ||
dependencies = [ | ||
('Python', '3.10.4'), # includes cffi | ||
# tensorflow~=2.10.0 required by medaka 1.9.1, see requirements.txt | ||
('TensorFlow', '2.11.0'), | ||
('Pysam', '0.19.1'), | ||
('SAMtools', '1.16.1'), | ||
('minimap2', _minimap_ver), | ||
('HTSlib', '1.15.1'), # for tabix, bgzip | ||
('Racon', '1.5.0'), | ||
('edlib', '1.3.9'), | ||
('pyspoa', '0.0.9'), | ||
('python-parasail', '1.3.3'), | ||
('ont-fast5-api', '4.1.1'), | ||
('WhatsHap', '1.7'), | ||
('intervaltree-python', '3.1.0'), | ||
('BCFtools', '1.15.1'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('mappy', _minimap_ver, { | ||
'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], | ||
}), | ||
(name, version, { | ||
'checksums': ['1018c07267d24cb4607ae823ced01a1789939b5f8143d1c240ce243dc1160ef5'], | ||
# remove TensorFlow version requirement which is too strict | ||
'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ", | ||
}), | ||
] | ||
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sanity_pip_check = True | ||
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sanity_check_paths = { | ||
'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], | ||
'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
} | ||
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sanity_check_commands = [ | ||
"medaka --help", | ||
"medaka_version_report", | ||
] | ||
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moduleclass = 'bio' |