##############################################################################
# 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 LICENSE file 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 *
from glob import glob


class PerlStarFusion(Package):
    """STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis
    Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate
    fusion transcripts supported by Illumina reads. STAR-Fusion further
    processes the output generated by the STAR aligner to map junction reads
    and spanning reads to a reference annotation set."""

    homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
    git      = "https://github.com/STAR-Fusion/STAR-Fusion.git"

    version('master', commit='a16a0a8')

    extends('perl')

    depends_on('star', type=('build', 'run'))
    depends_on('perl', type=('build', 'run'))
    depends_on('perl-intervaltree', type=('build', 'run'))
    depends_on('perl-dbi', type=('build', 'run'))
    depends_on('perl-dbfile', type=('build', 'run'))
    depends_on('perl-uri-escape', type=('build', 'run'))

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install('STAR-Fusion', prefix.bin)
        mkdirp(perl_lib_dir)
        with working_dir('PerlLib'):
            for pm in glob("*.pm"):
                install(pm, perl_lib_dir)
        with working_dir('util'):
            for files in glob("*"):
                install(files, prefix.bin)
