##############################################################################
# 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 RGviz(RPackage):
    """Genomic data analyses requires integrated visualization
    of known genomic information and new experimental data. Gviz
    uses the biomaRt and the rtracklayer packages to perform live
    annotation queries to Ensembl and UCSC and translates this to
    e.g. gene/transcript structures in viewports of the grid
    graphics package. This results in genomic information plotted
    together with your data."""

    homepage = "http://bioconductor.org/packages/Gviz/"
    git      = "https://git.bioconductor.org/packages/Gviz.git"

    version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')

    depends_on('r@3.4.0:3.4.9', when='@1.20.0')
    depends_on('r-s4vectors', type=('build', 'run'))
    depends_on('r-iranges', type=('build', 'run'))
    depends_on('r-genomicranges', type=('build', 'run'))
    depends_on('r-xvector', type=('build', 'run'))
    depends_on('r-rtracklayer', type=('build', 'run'))
    depends_on('r-lattice', type=('build', 'run'))
    depends_on('r-rcolorbrewer', type=('build', 'run'))
    depends_on('r-biomart', type=('build', 'run'))
    depends_on('r-annotationdbi', type=('build', 'run'))
    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-genomicfeatures', type=('build', 'run'))
    depends_on('r-bsgenome', type=('build', 'run'))
    depends_on('r-biostrings', type=('build', 'run'))
    depends_on('r-biovizbase', type=('build', 'run'))
    depends_on('r-rsamtools', type=('build', 'run'))
    depends_on('r-latticeextra', type=('build', 'run'))
    depends_on('r-matrixstats', type=('build', 'run'))
    depends_on('r-genomicalignments', type=('build', 'run'))
    depends_on('r-genomeinfodb', type=('build', 'run'))
    depends_on('r-biocgenerics', type=('build', 'run'))
    depends_on('r-digest', type=('build', 'run'))
