# Copyright 2013-2022 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 RDeseq2(RPackage):
    """Differential gene expression analysis based on the negative binomial
       distribution.

       Estimate variance-mean dependence in count data from high-throughput
       sequencing assays and test for differential expression based on a model
       using the negative binomial distribution."""

    homepage = "https://bioconductor.org/packages/DESeq2"
    git      = "https://git.bioconductor.org/packages/DESeq2.git"

    version('1.34.0', commit='25d4f74be59548122ccfbe8687d30c0bae5cf49a')
    version('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77')
    version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
    version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce')
    version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
    version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
    version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb')

    depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
    depends_on('r-s4vectors@0.23.18:', type=('build', 'run'), when='@1.30.0:')
    depends_on('r-iranges', type=('build', 'run'))
    depends_on('r-genomicranges', type=('build', 'run'))
    depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run'))
    depends_on('r-biocgenerics@0.7.5:', type=('build', 'run'))
    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-biocparallel', type=('build', 'run'))
    depends_on('r-genefilter', type=('build', 'run'))
    depends_on('r-locfit', type=('build', 'run'))
    depends_on('r-geneplotter', type=('build', 'run'))
    depends_on('r-ggplot2', type=('build', 'run'))
    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
    depends_on('r-rcpparmadillo', type=('build', 'run'))

    depends_on('r-hmisc', type=('build', 'run'), when='@:1.30.0')