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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Bamutil(MakefilePackage):
"""bamUtil is a repository that contains several programs
that perform operations on SAM/BAM files. All of these programs
are built into a single executable, bam.
"""
homepage = "https://genome.sph.umich.edu/wiki/BamUtil"
url = "https://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
version('1.0.13', sha256='16c1d01c37d1f98b98c144f3dd0fda6068c1902f06bd0989f36ce425eb0c592b')
depends_on('zlib', type=('build', 'link'))
# Looks like this will be fixed in 1.0.14.
# https://github.com/statgen/libStatGen/issues/9
patch('libstatgen-issue-9.patch', when='@1.0.13:')
# These are fixed in the standalone libStatGen,
# but bamutil@1.0.13 embeds its own copy, so fix 'em here.
patch('libstatgen-issue-19.patch', when='@1.0.13')
patch('libstatgen-issue-17.patch', when='@1.0.13')
patch('libstatgen-issue-7.patch', when='@1.0.13')
patch('verifybamid-issue-8.patch', when='@1.0.13')
parallel = False
@property
def install_targets(self):
return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]
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