60 lines
2.4 KiB
Python
60 lines
2.4 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/llnl/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 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 = "https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz"
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version('2.0.2', 'bb3f8cebf121312bf81789d963b4ecc5')
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version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
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depends_on('autoconf', type='build')
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depends_on('automake', type='build')
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depends_on('mpi')
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depends_on('boost@:1.50.0,1.53.0:', when='@2.0.2:')
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depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
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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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