spack/var/spack/repos/builtin/packages/abyss/package.py

# 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')