old_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 Bwa(Package):
      """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
  
      homepage = "http://github.com/lh3/bwa"
      url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
  
      version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
  
      depends_on('zlib')
  
      def install(self, spec, prefix):
          filter_file(r'^INCLUDES=',
                      "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
          filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
                      'Makefile')
          make()
  
          mkdirp(prefix.bin)
          install('bwa', join_path(prefix.bin, 'bwa'))
          set_executable(join_path(prefix.bin, 'bwa'))
          mkdirp(prefix.doc)
          install('README.md', prefix.doc)
          install('NEWS.md', prefix.doc)
          mkdirp(prefix.man1)
          install('bwa.1', prefix.man1)
  
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 Bwa(Package):
      """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
  
      homepage = "http://github.com/lh3/bwa"
      url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
  
      version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
      version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
              url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')
  
      depends_on('zlib')
  
      def install(self, spec, prefix):
          filter_file(r'^INCLUDES=',
                      "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
          filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
                      'Makefile')
          make()
  
          mkdirp(prefix.bin)
          install('bwa', join_path(prefix.bin, 'bwa'))
          set_executable(join_path(prefix.bin, 'bwa'))
          mkdirp(prefix.doc)
          install('README.md', prefix.doc)
          install('NEWS.md', prefix.doc)
          mkdirp(prefix.man1)
          install('bwa.1', prefix.man1)
  
subject: Add info for bwa@0.7.12 (#4356)