b306493884
* Fix digest for abyss@1.5.2 The digest value for v1.5.2 appears to have changed. This value works for me, today. The existing value v2.0.2 works as is. * Use "download" URL for ABYSS Following the suggestion of the project team, switch to using the release tarballs from the "download" URL instead of the automagically generated ones at the "archive" URL. Converstation here: https://github.com/bcgsc/abyss/issues/232
61 lines
2.5 KiB
Python
61 lines
2.5 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 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/releases/download/1.5.2/abyss-1.5.2.tar.gz"
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version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
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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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depends_on('libtool')
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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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