r-genomicalignments: created new package (#5785)
* r-genomicalignments: created new package * r-genomicalignments: using git repo source instead
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##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class RGenomicalignments(RPackage):
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"""Provides efficient containers for storing and manipulating short genomic
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alignments (typically obtained by aligning short reads to a reference
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genome). This includes read counting, computing the coverage, junction
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detection, and working with the nucleotide content of the alignments."""
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homepage = "https://bioconductor.org/packages/GenomicAlignments/"
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url = "https://git.bioconductor.org/packages/GenomicAlignments"
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list_url = homepage
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version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
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depends_on('r-biocgenerics', type=('build', 'run'))
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depends_on('r-s4vectors', type=('build', 'run'))
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depends_on('r-iranges', type=('build', 'run'))
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depends_on('r-genomeinfodb', type=('build', 'run'))
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depends_on('r-genomicranges', type=('build', 'run'))
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depends_on('r-summarizedexperiment', type=('build', 'run'))
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depends_on('r-biostrings', type=('build', 'run'))
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depends_on('r-rsamtools', type=('build', 'run'))
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depends_on('r-biocparallel', type=('build', 'run'))
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depends_on('r@3.4.0:3.4.9', when='@1.12.2')
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