Add abyss package (#4555)
* abyss * abyss: deleting attemped test from script * abyss: adding new package abyss * abyss: partially fixing mpi dependency issue * abyss: added mpi provider conflicts
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var/spack/repos/builtin/packages/abyss/package.py
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var/spack/repos/builtin/packages/abyss/package.py
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##############################################################################
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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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class Abyss(AutotoolsPackage):
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"""ABySS is a de novo, parallel, paired-end sequence assembler
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that is designed for short reads. The single-processor version
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is useful for assembling genomes up to 100 Mbases in size."""
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homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
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url = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz"
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version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
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depends_on('mpi')
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depends_on('boost@:1.50.0,1.53.0:')
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depends_on('sparsehash')
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depends_on('sqlite')
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conflicts('^intel-mpi')
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conflicts('^intel-parallel-studio+mpi')
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conflicts('^mvapich2')
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conflicts('^spectrum-mpi')
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def configure_args(self):
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args = ['--with-boost=%s' % self.spec['boost'].prefix,
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'--with-sqlite=%s' % self.spec['sqlite'].prefix,
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'--with-mpi=%s' % self.spec['mpi'].prefix]
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if self.spec['mpi'].name == 'mpich':
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args.append('--enable-mpich')
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return args
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