55 lines
2.3 KiB
Python
55 lines
2.3 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, 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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import os.path
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class Haploview(Package):
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"""Haploview is designed to simplify and expedite the process of haplotype
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analysis."""
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homepage = "http://www.broadinstitute.org/haploview/haploview"
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url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar"
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version('4.1', 'f7aa4accda5fad1be74c9c1969c6ee7d', expand=False)
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depends_on('java', type=('build', 'run'))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'Haploview{v}.jar'.format(v=self.version)
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install(jar_file, prefix.bin)
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script_sh = join_path(os.path.dirname(__file__), "haploview.sh")
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script = prefix.bin.haploview
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install(script_sh, script)
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set_executable(script)
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java = 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('haploview.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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