54 lines
2.2 KiB
Python
54 lines
2.2 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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class Soapindel(MakefilePackage):
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"""SOAPindel is focusing on calling indels from the next-generation
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paired-end sequencing data."""
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homepage = "http://soap.genomics.org.cn/soapindel.html"
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version('2.1.7.17', '317ef494173969cdc6a8244dd87d06bd',
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url='http://soap.genomics.org.cn/down/SOAPindel_20130918_2.1.7.17.zip')
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depends_on('perl', type=('build', 'run'))
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build_directory = 'indel_detection.release'
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def install(self, spec, prefix):
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with working_dir('indel_detection.release'):
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install_tree('tools', prefix.tools)
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mkdirp(prefix.lib)
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install('affine_align.pm', prefix.lib)
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install('indel_lib.pm', prefix.lib)
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mkdirp(prefix.bin)
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install('assemble_align', prefix.bin)
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install('cluster_reads', prefix.bin)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PERL5LIB', self.prefix.lib)
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run_env.prepend_path('PATH', self.prefix.tools)
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