##############################################################################
# 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/llnl/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 Bwa(Package):
    """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""

    homepage = "http://github.com/lh3/bwa"
    url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"

    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554',
            url="https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2")
    version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
            url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')

    depends_on('zlib')

    def install(self, spec, prefix):
        filter_file(r'^INCLUDES=',
                    "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
        filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
                    'Makefile')
        make()

        mkdirp(prefix.bin)
        install('bwa', join_path(prefix.bin, 'bwa'))
        set_executable(join_path(prefix.bin, 'bwa'))
        mkdirp(prefix.doc)
        install('README.md', prefix.doc)
        install('NEWS.md', prefix.doc)
        mkdirp(prefix.man.man1)
        install('bwa.1', prefix.man.man1)

##############################################################################
# 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/llnl/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 Bwa(Package):
    """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""

    homepage = "http://github.com/lh3/bwa"
    url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"

    version('0.7.17', '82cba7ef695538e6a38b9d4156837381',
            url="https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2")
    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554',
            url="https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2")
    version('0.7.13', 'f094f609438511766c434178a3635ab4',
            url="https://github.com/lh3/bwa/releases/download/v0.7.13/bwa-0.7.13.tar.bz2")
    version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
            url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')

    depends_on('zlib')

    def install(self, spec, prefix):
        filter_file(r'^INCLUDES=',
                    "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
        filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
                    'Makefile')
        make()

        mkdirp(prefix.bin)
        install('bwa', join_path(prefix.bin, 'bwa'))
        set_executable(join_path(prefix.bin, 'bwa'))
        mkdirp(prefix.doc)
        install('README.md', prefix.doc)
        install('NEWS.md', prefix.doc)
        mkdirp(prefix.man.man1)
        install('bwa.1', prefix.man.man1)

add 0.7.17 (#5902)