d8b6859e7b
See the discussion about installing jar files in #4386. Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.
76 lines
3.3 KiB
Python
76 lines
3.3 KiB
Python
##############################################################################
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# Copyright (c) 2013-2016, 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/llnl/spack
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# Please also see the LICENSE file 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 Picard(Package):
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"""Picard is a set of command line tools for manipulating high-throughput
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sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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"""
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homepage = "http://broadinstitute.github.io/picard/"
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url = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar"
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# They started distributing a single jar file at v2.6.0, prior to
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# that it was a .zip file with multiple .jar and .so files
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version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False,
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url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar")
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version('1.140', '308f95516d94c1f3273a4e7e2b315ec2',
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url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip')
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depends_on('jdk@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__), "picard.sh")
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script = join_path(prefix.bin, "picard")
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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['jdk'].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('picard.jar', join_path(prefix.bin, 'picard.jar'),
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script, **kwargs)
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def setup_environment(self, spack_env, run_env):
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"""The Picard docs suggest setting this as a convenience."""
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run_env.prepend_path('PICARD',
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join_path(self.prefix, 'bin', 'picard.jar'))
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