37 lines
1.3 KiB
Python
37 lines
1.3 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Bamutil(MakefilePackage):
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"""bamUtil is a repository that contains several programs
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that perform operations on SAM/BAM files. All of these programs
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are built into a single executable, bam.
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"""
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homepage = "http://genome.sph.umich.edu/wiki/BamUtil"
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url = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
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version('1.0.13', sha256='16c1d01c37d1f98b98c144f3dd0fda6068c1902f06bd0989f36ce425eb0c592b')
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depends_on('zlib', type=('build', 'link'))
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# Looks like this will be fixed in 1.0.14.
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# https://github.com/statgen/libStatGen/issues/9
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patch('libstatgen-issue-9.patch', when='@1.0.13:')
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# These are fixed in the standalone libStatGen,
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# but bamutil@1.0.13 embeds its own copy, so fix 'em here.
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patch('libstatgen-issue-19.patch', when='@1.0.13')
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patch('libstatgen-issue-17.patch', when='@1.0.13')
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patch('libstatgen-issue-7.patch', when='@1.0.13')
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patch('verifybamid-issue-8.patch', when='@1.0.13')
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parallel = False
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@property
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def install_targets(self):
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return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]
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