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 Bracken(Package):
      """Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
      accurate statistical method that computes the abundance of species in DNA
      sequences from a metagenomics sample."""
  
      homepage = "https://ccb.jhu.edu/software/bracken"
      url      = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
  
      version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d')
  
      depends_on('perl')
      depends_on('python@2.7:')
      depends_on('perl-exporter-tiny')
      depends_on('perl-list-moreutils')
      depends_on('perl-parallel-forkmanager')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install_tree('sample_data', prefix.sample_data)
  
          filter_file(
              r'#!/bin/env perl',
              '#!/usr/bin/env perl',
              'count-kmer-abundances.pl'
          )
  
          filter_file(
              r'#!/usr/bin/python',
              '#!/usr/bin/env python',
              'est_abundance.py'
          )
  
          filter_file(
              r'#!/usr/bin/python',
              '#!/usr/bin/env python',
              'generate_kmer_distribution.py'
          )
  
          files = (
              'count-kmer-abundances.pl',
              'est_abundance.py',
              'generate_kmer_distribution.py',
          )
  
          chmod = which('chmod')
          for name in files:
              install(name, prefix.bin)
              chmod('+x', join_path(self.prefix.bin, name))
  
subject: Create new package (#7375)