39 lines
1.4 KiB
Python
39 lines
1.4 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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import os.path
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class Pgdspider(Package):
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""""PGDSpider is a powerful automated data conversion tool for population
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genetic and genomics programs"""
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homepage = "http://www.cmpg.unibe.ch/software/PGDSpider"
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url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_2.1.1.2.zip"
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version('2.1.1.2', sha256='a630ef9f3ef0c36be0d613867c5293378d77b52396ac701bc7b9ec5d3ba7f2e1')
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depends_on('java', type=('build', 'run'))
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depends_on('bcftools')
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depends_on('bwa')
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depends_on('samtools')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'PGDSpider{0}-cli.jar'.format(self.version.up_to(1))
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install(jar_file, prefix.bin)
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script_sh = join_path(os.path.dirname(__file__), "pgdspider.sh")
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script = prefix.bin.pgdspider
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install(script_sh, script)
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set_executable(script)
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java = self.spec['java'].prefix.bin.java
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kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('pgdspider.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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