##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
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