73 lines
3.1 KiB
Python
73 lines
3.1 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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from shutil import copyfile
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import glob
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import os.path
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import re
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class Gatk(Package):
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"""Genome Analysis Toolkit
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Variant Discovery in High-Throughput Sequencing Data
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"""
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homepage = "http://broadinstitute.github.io/gatk/"
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url = "https://software.broadinstitute.org/gatk/download/auth?package=GATK"
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_urlfmt = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz"
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version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
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url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
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depends_on('java@8:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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# The list of files to install varies with release...
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# ... but skip the spack-{build.env}.out files.
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files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
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for f in files:
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install(f, prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
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script = join_path(prefix.bin, "gatk")
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copyfile(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = join_path(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('GenomeAnalysisTK.jar', join_path(prefix.bin,
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'GenomeAnalysisTK.jar'),
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script, **kwargs)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('GATK',
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join_path(self.prefix, 'bin',
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'GenomeAnalysisTK.jar'))
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