new_contents: ##############################################################################
  # Copyright (c) 2013-2016, 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/llnl/spack
  # Please also see the LICENSE file 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 Abyss(AutotoolsPackage):
      """ABySS is a de novo, parallel, paired-end sequence assembler
         that is designed for short reads. The single-processor version
         is useful for assembling genomes up to 100 Mbases in size."""
  
      homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
      url      = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz"
  
      version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
  
      depends_on('mpi')
      depends_on('boost@:1.50.0,1.53.0:')
      depends_on('sparsehash')
      depends_on('sqlite')
  
      conflicts('^intel-mpi')
      conflicts('^intel-parallel-studio+mpi')
      conflicts('^mvapich2')
      conflicts('^spectrum-mpi')
  
      def configure_args(self):
          args = ['--with-boost=%s' % self.spec['boost'].prefix,
                  '--with-sqlite=%s' % self.spec['sqlite'].prefix,
                  '--with-mpi=%s' % self.spec['mpi'].prefix]
          if self.spec['mpi'].name == 'mpich':
                  args.append('--enable-mpich')
          return args
  
subject: Add abyss package (#4555)