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 Libbeagle(AutotoolsPackage):
      """Beagle performs genotype calling, genotype phasing, imputation of
         ungenotyped markers, and identity-by-descent segment detection."""
  
      homepage = "https://github.com/beagle-dev/beagle-lib"
      url      = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz"
  
      version('2.1.2', '1107614e86f652f8ee45c1c92f2af3d4')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
  
      depends_on('subversion', type='build')
      depends_on('pkgconfig', type='build')
  
      def url_for_version(self, version):
          url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
          return url.format(version.underscored)
  
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 Libbeagle(AutotoolsPackage):
      """Beagle performs genotype calling, genotype phasing, imputation of
         ungenotyped markers, and identity-by-descent segment detection."""
  
      homepage = "https://github.com/beagle-dev/beagle-lib"
      url      = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz"
  
      version('2.1.2', '1107614e86f652f8ee45c1c92f2af3d4')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
  
      depends_on('subversion', type='build')
      depends_on('pkgconfig', type='build')
      depends_on('java', type='build')
  
      def url_for_version(self, version):
          url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
          return url.format(version.underscored)
  
      def setup_environment(self, spack_env, run_env):
          prefix = self.prefix
          run_env.prepend_path('BEAST_LIB', prefix.lib)
  
subject: add java dependency so jni hooks get built (#8524)