8977f7377a
* abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: Revise the points indicated by the review.
62 lines
2.2 KiB
Python
62 lines
2.2 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import numbers
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from spack import *
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def is_multiple_32(x):
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"""multiple of 32 """
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try:
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return isinstance(int(x), numbers.Integral) and \
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not isinstance(x, bool) and int(x) % 32 == 0
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except ValueError:
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return False
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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('2.1.4', sha256='2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc')
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version('2.0.2', sha256='d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df')
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version('1.5.2', sha256='8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1')
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variant('maxk', default=128, values=is_multiple_32,
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description='set the maximum k-mer length.')
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depends_on('autoconf', type='build')
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depends_on('automake', type='build')
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depends_on('bwa', type='run')
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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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maxk = int(self.spec.variants['maxk'].value)
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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 maxk:
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args.append('--enable-maxk=%s' % maxk)
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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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patch('fix_BloomFilter.hpp.patch', when='@2.0.0:2.1.4')
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