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