##############################################################################
# Copyright (c) 2013-2018, 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 Casper(MakefilePackage):
    """CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art
       merging tool in terms of accuracy and robustness. Using this
       sophisticated merging method, we could get elongated reads from the
       forward and reverse reads."""

    homepage = "http://best.snu.ac.kr/casper/index.php?name=main"
    url      = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz"

    version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2')

    depends_on('jellyfish@2.2.3:')
    depends_on('boost')

    conflicts('%gcc@7.1.0')

    def install(self, spec, prefix):
        install_tree('.', prefix)

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