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 Redundans(Package):
      """Redundans pipeline assists an assembly of heterozygous genomes."""
  
      homepage = "https://github.com/Gabaldonlab/redundans"
      url      = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
  
      version('0.13c', '2003fb7c70521f5e430553686fd1a594')
  
      depends_on('python', type=('build', 'run'))
      depends_on('py-pyscaf', type=('build', 'run'))
      depends_on('py-fastaindex', type=('build', 'run'))
      depends_on('perl', type=('build', 'run'))
      depends_on('sspace-standard')
      depends_on('bwa')
      depends_on('last')
      depends_on('gapcloser')
      depends_on('parallel')
      depends_on('snap-berkeley')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install('redundans.py', prefix.bin)
          with working_dir('bin'):
              install('fasta2homozygous.py', prefix.bin)
              install('fasta2split.py', prefix.bin)
              install('fastq2insert_size.py', prefix.bin)
              install('fastq2mates.py', prefix.bin)
              install('fastq2shuffled.py', prefix.bin)
              install('fastq2sspace.py', prefix.bin)
              install('filterReads.py', prefix.bin)
  
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 Redundans(Package):
      """Redundans pipeline assists an assembly of heterozygous genomes."""
  
      homepage = "https://github.com/Gabaldonlab/redundans"
      url      = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
  
      version('0.13c', '2003fb7c70521f5e430553686fd1a594')
  
      depends_on('python', type=('build', 'run'))
      depends_on('py-pyscaf', type=('build', 'run'))
      depends_on('py-fastaindex', type=('build', 'run'))
      depends_on('py-numpy', type=('build', 'run'))
      depends_on('perl', type=('build', 'run'))
      depends_on('sspace-standard')
      depends_on('bwa')
      depends_on('last')
      depends_on('gapcloser')
      depends_on('parallel')
      depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install('redundans.py', prefix.bin)
          with working_dir('bin'):
              install('fasta2homozygous.py', prefix.bin)
              install('fasta2split.py', prefix.bin)
              install('fastq2insert_size.py', prefix.bin)
              install('fastq2mates.py', prefix.bin)
              install('fastq2shuffled.py', prefix.bin)
              install('fastq2sspace.py', prefix.bin)
              install('filterReads.py', prefix.bin)
  
subject: add py-numpy dep, snap-berkeley version constraint (#9354)