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r-genomicranges: added new package (#5697)

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Yifan Zhu 2017-10-11 20:45:03 -05:00 committed by Christoph Junghans
parent c93ecda872
commit dc95dddd61
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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 RGenomicranges(RPackage):
"""The ability to efficiently represent and manipulate genomic annotations
and alignments is playing a central role when it comes to analyzing
high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges
package defines general purpose containers for storing and manipulating
genomic intervals and variables defined along a genome. More specialized
containers for representing and manipulating short alignments against a
reference genome, or a matrix-like summarization of an experiment, are
defined in the GenomicAlignments and SummarizedExperiment packages
respectively. Both packages build on top of the GenomicRanges
infrastructure."""
homepage = "https://bioconductor.org/packages/GenomicRanges/"
url = "https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.5.tar.gz"
list_url = homepage
version('1.28.6', '84c5a40e846b35e98d019ca39783cfe6')
version('1.28.5', '5b11897331c4371e09133ea3be125c03')
depends_on('r-biocgenerics', 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-xvector', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.28.5:1.28.6')