old_contents: ##############################################################################
  # Copyright (c) 2013-2018, 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 RGenomicalignments(RPackage):
      """Provides efficient containers for storing and manipulating short genomic
      alignments (typically obtained by aligning short reads to a reference
      genome). This includes read counting, computing the coverage, junction
      detection, and working with the nucleotide content of the alignments."""
  
      homepage = "https://bioconductor.org/packages/GenomicAlignments/"
      url      = "https://git.bioconductor.org/packages/GenomicAlignments"
      list_url = homepage
  
      version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
  
      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-genomicranges', type=('build', 'run'))
      depends_on('r-summarizedexperiment', type=('build', 'run'))
      depends_on('r-biostrings', type=('build', 'run'))
      depends_on('r-rsamtools', type=('build', 'run'))
      depends_on('r-biocparallel', type=('build', 'run'))
      depends_on('r@3.4.0:3.4.9', when='@1.12.2')
  
new_contents: ##############################################################################
  # Copyright (c) 2013-2018, 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 RGenomicalignments(RPackage):
      """Provides efficient containers for storing and manipulating short genomic
      alignments (typically obtained by aligning short reads to a reference
      genome). This includes read counting, computing the coverage, junction
      detection, and working with the nucleotide content of the alignments."""
  
      homepage = "https://bioconductor.org/packages/GenomicAlignments/"
      url      = "https://git.bioconductor.org/packages/GenomicAlignments"
      list_url = homepage
  
      version('1.14.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
      version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
  
      depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
      depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
      depends_on('r-iranges@2.5.36:', type=('build', 'run'), when='@1.12.2')
      depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.14.2')
      depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'), when='@1.12.2')
      depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.14.2')
      depends_on('r-genomicranges@1.27.19:', type=('build', 'run'), when='@1.12.2')
      depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.14.2')
      depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
      depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
      depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
      depends_on('r-biocparallel', type=('build', 'run'))
      depends_on('r@3.4.0:3.4.9', when='@1.12.2:')
  
subject: package update (#7791)