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# Copyright 2013-2022 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)
import numbers
from spack import *
from spack.pkg.builtin.boost import Boost
def is_multiple_32(x):
"""multiple of 32 """
try:
return isinstance(int(x), numbers.Integral) and \
not isinstance(x, bool) and int(x) % 32 == 0
except ValueError:
return False
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 = "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
url = "https://github.com/bcgsc/abyss/releases/download/2.3.1/abyss-2.3.1.tar.gz"
version('2.3.1', sha256='664045e7903e9732411effc38edb9ebb1a0c1b7636c64b3a14a681f465f43677')
version('2.3.0', sha256='3df923b0699187fb27948cae43293eeb5745161d5dc484b9befbe2ca8efb6ad7')
version('2.2.5', sha256='38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521')
version('2.1.4', sha256='2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc')
version('2.0.2', sha256='d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df')
version('1.5.2', sha256='8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1')
variant('maxk', default=128, values=is_multiple_32,
description='set the maximum k-mer length.')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('bwa', type='run')
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')
# Maintainers: Is boost really a dependency? In what conditions?
depends_on(Boost.with_default_variants)
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
patch('fix_BloomFilter.hpp.patch', when='@2.0.0:2.1.4')
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