61 lines
2.6 KiB
Python
61 lines
2.6 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 os.path
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class Pilon(Package):
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"""Pilon is an automated genome assembly improvement and variant
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detection tool."""
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homepage = "https://github.com/broadinstitute/pilon"
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url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
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version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
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version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
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depends_on('java@1.7:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'pilon-{0}.jar'.format(self.version.dotted)
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install(jar_file, 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__), "pilon.sh")
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script = join_path(prefix.bin, "pilon")
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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('pilon-{0}.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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