##############################################################################
# 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 SoapdenovoTrans(MakefilePackage):
    """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
       SOAPdenovo framework, adapt to alternative splicing and different
       expression level among transcripts."""

    homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
    url      = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"

    version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')

    build_directory = 'src'

    def edit(self, spec, prefix):
        with working_dir(self.build_directory):
            makefile = FileFilter('Makefile')
            makefile.filter('CFLAGS=         -O3 -fomit-frame-pointer -static',
                            'CFLAGS=         -O3 -fomit-frame-pointer')

    def build(self, spec, prefix):
        with working_dir(self.build_directory):
            make()
            make('127mer=1', parallel=False)

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