##############################################################################
# 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 *
import distutils.dir_util


class Mefit(Package):
    """This pipeline will merge overlapping paired-end reads, calculate
    merge statistics, and filter reads for quality."""

    homepage = "https://github.com/nisheth/MeFiT"
    url      = "https://github.com/nisheth/MeFiT.git"

    version('1.0', git='https://github.com/nisheth/MeFiT.git', commit='0733326d8917570bbf70ff5c0f710bf66c13db09')

    depends_on('py-numpy')
    depends_on('py-htseq')
    depends_on('jellyfish')
    depends_on('casper %gcc@4.8.5')

    def install(self, spec, prefix):
        distutils.dir_util.copy_tree(".", prefix)

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