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r-rsamtools: created new package (#5702)

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Yifan Zhu 2017-10-11 20:42:55 -05:00 committed by Christoph Junghans
parent 670463e95a
commit 01e104dfcb
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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 RRsamtools(RPackage):
"""This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence
Alignment / Map), FASTA, binary variant call (BCF) and compressed
indexed tab-delimited (tabix) files."""
homepage = "https://bioconductor.org/packages/Rsamtools/"
url = "https://bioconductor.org/packages/3.5/bioc/src/contrib/Rsamtools_1.28.0.tar.gz"
list_url = homepage
version('1.28.0', '313bceac68edec07f2ee466520461d35')
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-bitops', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.28.0')