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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Abyss(AutotoolsPackage):
"""ABySS is a de novo, parallel, paired-end sequence assembler
that is designed for short reads. The single-processor version
is useful for assembling genomes up to 100 Mbases in size."""
homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
url = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz"
version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
variant('maxk', values=int, default=0,
description='''set the maximum k-mer length.
This value must be a multiple of 32''')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('mpi')
depends_on('boost@:1.50.0,1.53.0:', when='@2.0.2:')
depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
depends_on('sparsehash')
depends_on('sqlite')
depends_on('libtool')
conflicts('^intel-mpi')
conflicts('^intel-parallel-studio+mpi')
conflicts('^mvapich2')
conflicts('^spectrum-mpi')
def configure_args(self):
maxk = int(self.spec.variants['maxk'].value)
args = ['--with-boost=%s' % self.spec['boost'].prefix,
'--with-sqlite=%s' % self.spec['sqlite'].prefix,
'--with-mpi=%s' % self.spec['mpi'].prefix]
if maxk:
args.append('--enable-maxk=%s' % maxk)
if self.spec['mpi'].name == 'mpich':
args.append('--enable-mpich')
return args
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