##############################################################################
# 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 PacbioDaligner(MakefilePackage):
    """Daligner: The Dazzler "Overlap" Module. This is a special fork
       required for some pacbio utilities."""

    homepage = "https://github.com/PacificBiosciences/DALIGNER"
    url      = "https://github.com/PacificBiosciences/DALIGNER"

    version('2017-08-05',
            git='https://github.com/PacificBiosciences/DALIGNER.git',
            commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')

    depends_on('gmake', type='build')
    depends_on('pacbio-dazz-db')

    def edit(self, spec, prefix):
        mkdir(prefix.bin)
        makefile = FileFilter('Makefile')
        makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
        gmf = FileFilter('GNUmakefile')
        gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
                   'cp ${ALL} ' + prefix.bin)