##############################################################################
# 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 Stringtie(MakefilePackage):
    """StringTie is a fast and highly efficient assembler of RNA-Seq alignments
       into potential transcripts."""

    homepage = "https://ccb.jhu.edu/software/stringtie"
    url      = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz"

    version('1.3.3b', '11a43260b18e4272182380e922445d88')

    depends_on('samtools')

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

##############################################################################
# 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 Stringtie(MakefilePackage):
    """StringTie is a fast and highly efficient assembler of RNA-Seq alignments
       into potential transcripts."""

    homepage = "https://ccb.jhu.edu/software/stringtie"
    url      = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz"

    version('1.3.4a', '2a191ef6512242a3a5778cf7718bb6af')
    version('1.3.3b', '11a43260b18e4272182380e922445d88')

    depends_on('samtools')

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

add version 1.3.4a (#7164)