##############################################################################
# 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 Orthomcl(Package):
    """OrthoMCL is a genome-scale algorithm for grouping orthologous protein
       sequences."""

    homepage = "http://orthomcl.org/orthomcl/"
    url      = "http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz"

    version('2.0.9', '2e0202ed4e36a753752c3567edb9bba9')

    depends_on('perl', type=('build', 'run'))
    depends_on('blast-plus')
    depends_on('mcl')
    depends_on('mariadb')

    def install(self, spec, prefix):
        install_tree('bin', prefix.bin)
        install_tree('config', prefix.config)
        install_tree('doc', prefix.doc)
        install_tree('lib', prefix.lib)

    def setup_environment(self, spack_env, run_env):
        run_env.prepend_path('PERL5LIB', self.prefix.lib)