# 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 RSomaticsignatures(RPackage):
    """The SomaticSignatures package identifies mutational signatures of
       single nucleotide variants (SNVs). It provides a infrastructure related
       to the methodology described in Nik-Zainal (2012, Cell), with
       flexibility in the matrix decomposition algorithms."""

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

    version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a')

    depends_on('r-variantannotation', type=('build', 'run'))
    depends_on('r-genomicranges', type=('build', 'run'))
    depends_on('r-nmf', type=('build', 'run'))
    depends_on('r-s4vectors', type=('build', 'run'))
    depends_on('r-iranges', type=('build', 'run'))
    depends_on('r-genomeinfodb', type=('build', 'run'))
    depends_on('r-biostrings', type=('build', 'run'))
    depends_on('r-ggplot2', type=('build', 'run'))
    depends_on('r-ggbio', type=('build', 'run'))
    depends_on('r-reshape2', type=('build', 'run'))
    depends_on('r-pcamethods', type=('build', 'run'))
    depends_on('r-biobase', type=('build', 'run'))
    depends_on('r-proxy', type=('build', 'run'))
    depends_on('r@3.4.0:3.4.9', when='@2.12.1')