# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class RAllelicimbalance(RPackage):
    """Investigates Allele Specific Expression.

       Provides a framework for allelic specific expression investigation using
       RNA-seq data."""

    homepage = "https://bioconductor.org/packages/AllelicImbalance"
    git      = "https://git.bioconductor.org/packages/AllelicImbalance.git"

    version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
    version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3')
    version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea')
    version('1.16.0', commit='85f652ae8a0dd15535819b6e934065182df5544a')
    version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')

    depends_on('r@3.2.0:', type=('build', 'run'))
    depends_on('r-genomicranges', type=('build', 'run'))
    depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run'))
    depends_on('r-genomicalignments', type=('build', 'run'))
    depends_on('r-biocgenerics', type=('build', 'run'))
    depends_on('r-annotationdbi', type=('build', 'run'))
    depends_on('r-bsgenome', type=('build', 'run'))
    depends_on('r-variantannotation', type=('build', 'run'))
    depends_on('r-biostrings', type=('build', 'run'))
    depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
    depends_on('r-iranges', type=('build', 'run'))
    depends_on('r-rsamtools', type=('build', 'run'))
    depends_on('r-genomicfeatures', type=('build', 'run'))
    depends_on('r-gviz', type=('build', 'run'))
    depends_on('r-lattice', type=('build', 'run'))
    depends_on('r-latticeextra', type=('build', 'run'))
    depends_on('r-gridextra', type=('build', 'run'))
    depends_on('r-seqinr', type=('build', 'run'))
    depends_on('r-genomeinfodb', type=('build', 'run'))
    depends_on('r-nlme', type=('build', 'run'))

    depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run'))
    depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))

    depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run'))