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 Braker(Package):
      """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
         that combines the advantages of GeneMark-ET and AUGUSTUS"""
  
      homepage = "http://exon.gatech.edu/braker1.html"
      url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
      list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
  
      version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
      version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
              url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('augustus@3.2.3')
      depends_on('genemark-et')
      depends_on('bamtools')
      depends_on('samtools')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.lib)
          install('braker.pl', prefix.bin)
          install('filterGenemark.pl', prefix.bin)
          install('filterIntronsFindStrand.pl', prefix.bin)
          install('helpMod.pm', prefix.lib)
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PERL5LIB', prefix.lib)
  
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 Braker(Package):
      """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
         that combines the advantages of GeneMark-ET and AUGUSTUS"""
  
      homepage = "http://exon.gatech.edu/braker1.html"
      url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
      list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
  
      version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
      version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
              url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('perl-scalar-util-numeric', type=('build', 'run'))
      depends_on('perl-parallel-forkmanager', type=('build', 'run'))
      depends_on('perl-file-which', type=('build', 'run'))
      depends_on('augustus@3.2.3')
      depends_on('genemark-et')
      depends_on('bamtools')
      depends_on('samtools')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.lib)
          install('braker.pl', prefix.bin)
          install('filterGenemark.pl', prefix.bin)
          install('filterIntronsFindStrand.pl', prefix.bin)
          install('helpMod.pm', prefix.lib)
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PERL5LIB', prefix.lib)
  
subject: add missing deps (#9468)