# 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 RYarn(RPackage):
    """Robust Multi-Condition RNA-Seq Preprocessing and Normalization.

       Expedite large RNA-Seq analyses using a combination of previously
       developed tools. YARN is meant to make it easier for the user in
       performing basic mis-annotation quality control, filtering, and
       condition-aware normalization. YARN leverages many Bioconductor tools
       and statistical techniques to account for the large heterogeneity and
       sparsity found in very large RNA-seq experiments."""

    bioc = "yarn"

    version('1.20.0', commit='b41e4ef14f980518af2fc59f202ad8ec148e8b47')
    version('1.16.0', commit='ff5a18cb946ffec3cb773fe32af401c8a72d674a')
    version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472')
    version('1.8.1', commit='ee0723d4dbf082b4469ca9c22cce4f1a2ac81c04')
    version('1.6.0', commit='19d1b2ef275f294bd318b86e0d237c271880117d')
    version('1.4.0', commit='36100f40b9e520c072d0d5ebf963723b813f7db0')
    version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697')

    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-biomart', type=('build', 'run'))
    depends_on('r-downloader', type=('build', 'run'))
    depends_on('r-edger', type=('build', 'run'))
    depends_on('r-gplots', type=('build', 'run'))
    depends_on('r-limma', type=('build', 'run'))
    depends_on('r-matrixstats', type=('build', 'run'))
    depends_on('r-preprocesscore', type=('build', 'run'))
    depends_on('r-readr', type=('build', 'run'))
    depends_on('r-rcolorbrewer', type=('build', 'run'))
    depends_on('r-quantro', type=('build', 'run'))