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 Tophat(AutotoolsPackage):
      """Spliced read mapper for RNA-Seq."""
  
      homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
      url      = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
  
      version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
  
      depends_on('boost@1.47:')
      depends_on('bowtie2', type='run')
  
      parallel = False
  
      def configure_args(self):
          return ["--with-boost={0}".format(self.spec['boost'].prefix)]
  
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 Tophat(AutotoolsPackage):
      """Spliced read mapper for RNA-Seq."""
  
      homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
      url      = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
  
      version('2.1.2', 'db844fd7f53c519e716cd6222e6195b2')
      version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')
  
      depends_on('autoconf', type='build')
      # 2.1.1 only builds with automake@1.15.1.  There's a patch here:
      # https://github.com/spack/spack/pull/8244, which was incorporated
      # upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
      depends_on('automake',                        type='build')
      depends_on('automake@1.15.1', when='@:2.1.1', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
  
      depends_on('boost@1.47:')
      depends_on('bowtie2', type='run')
  
      parallel = False
  
      def configure_args(self):
          return ["--with-boost={0}".format(self.spec['boost'].prefix)]
  
subject: Add Tophat v2.1.2, fixes automake issues (#8266)