new_contents: ##############################################################################
  # 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'))
  
subject: Create new package. (#6332)