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


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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 Stacks(AutotoolsPackage):
    """Stacks is a software pipeline for building loci from short-read
       sequences, such as those generated on the Illumina platform."""

    homepage = "http://catchenlab.life.illinois.edu/stacks/"
    url      = "http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz"

    version('1.46', '18b0568a4bba44fb4e5be0eb7ee2c08d')

    variant('sparsehash', default=True, description='Improve Stacks memory usage with SparseHash')

    depends_on('perl', type=('build', 'run'))
    depends_on('sparsehash', when='+sparsehash')

    def configure_args(self):
        args = []
        if '+sparsehash' in self.spec:
            args.append('--enable-sparsehash')
        else:
            args.append('--disable-sparsehash')
        return args