##############################################################################
# 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 RAbaenrichment(RPackage):
    """The package ABAEnrichment is designed to test for enrichment
    of user defined candidate genes in the set of expressed genes in
    different human brain regions. The core function 'aba_enrich'
    integrates the expression of the candidate gene set (averaged
    across donors) and the structural information of the brain using
    an ontology, both provided by the Allen Brain Atlas project.
    'aba_enrich' interfaces the ontology enrichment software FUNC to
    perform the statistical analyses. Additional functions provided
    in this package like 'get_expression' and 'plot_expression'
    facilitate exploring the expression data. From version 1.3.5
    onwards genomic regions can be provided as input, too; and from
    version 1.5.9 onwards the function 'get_annotated_genes' offers
    an easy way to obtain annotations of genes to enriched or
    user-defined brain regions."""

    homepage = "https://bioconductor.org/packages/ABAEnrichment/"
    url      = "https://git.bioconductor.org/packages/ABAEnrichment"

    version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')

    depends_on('r@3.4.0:3.4.9', when='@1.6.0')
    depends_on('r-rcpp', type=('build', 'run'))
    depends_on('r-gplots', type=('build', 'run'))
    depends_on('r-gtools', type=('build', 'run'))
    depends_on('r-abadata', type=('build', 'run'))