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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
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', '170e5b4a002277ff66866486da920693')
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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