text: # Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class RGenomicalignments(RPackage):
      """Representation and manipulation of short genomic alignments.
  
         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"
      git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
  
      version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
      version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab')
      version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
      version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
      version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
  
      depends_on('r@2.10:', type=('build', 'run'))
      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'))
      depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
      depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
      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-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run'))
      depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
      depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run'))
  
      depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run'))
  
      depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run'))
      depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run'))
      depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run'))
  