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r-shortread: Create new package. (#6332)

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lingnanyuan 2017-11-16 10:30:18 -06:00 committed by Christoph Junghans
parent cca06422fa
commit e732a554ff
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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/spack/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 RShortread(RPackage):
"""This package implements sampling, iteration, and input of FASTQ
files. The package includes functions for filtering and trimming
reads, and for generating a quality assessment report. Data are
represented as DNAStringSet-derived objects, and easily manipulated
for a diversity of purposes. The package also contains legacy support
for early single-end, ungapped alignment formats."""
homepage = "https://www.bioconductor.org/packages/ShortRead/"
url = "https://git.bioconductor.org/packages/ShortRead"
version('1.34.2', git='https://git.bioconductor.org/packages/ShortRead', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
depends_on('r@3.4.0:3.4.9', when='@1.34.2')
depends_on('r-latticeextra', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-hwriter', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))