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r-yapsa: created new package (#6121)

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Yifan Zhu 2017-11-03 15:21:00 -05:00 committed by Christoph Junghans
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##############################################################################
# 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/llnl/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 RYapsa(RPackage):
"""This package provides functions and routines useful in the analysis of
somatic signatures (cf. L. Alexandrov et al., Nature 2013). In
particular, functions to perform a signature analysis with known
signatures (LCD = linear combination decomposition) and a signature
analysis on stratified mutational catalogue (SMC = stratify mutational
catalogue) are provided."""
homepage = "http://bioconductor.org/packages/YAPSA/"
url = "https://git.bioconductor.org/packages/YAPSA"
list_url = homepage
version('1.2.0', git='https://git.bioconductor.org/packages/YAPSA', commit='320809b69e470e30a777a383f8341f93064ec24d')
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-lsei', type=('build', 'run'))
depends_on('r-somaticsignatures', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-corrplot', type=('build', 'run'))
depends_on('r-dendextend', type=('build', 'run'))
depends_on('r-getoptlong', type=('build', 'run'))
depends_on('r-gtrellis', type=('build', 'run'))
depends_on('r-pmcmr', type=('build', 'run'))
depends_on('r-complexheatmap', type=('build', 'run'))
depends_on('r-keggrest', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.2.0')