old_contents: # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class Libbeagle(AutotoolsPackage, CudaPackage):
      """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 patch(self):
          # update cuda architecture if necessary
          if '+cuda' in self.spec:
              arch = self.spec.variants['cuda_arch'].value
              archflag = ''
  
              if arch[0] != 'none':
                  archflag = '-arch=%s' % arch[0]
  
              filter_file('-arch compute_13', archflag,
                          'libhmsbeagle/GPU/kernels/Makefile.am',
                          string=True)
  
              # point CUDA_LIBS to libcuda.so
              filter_file('-L$with_cuda/lib', '-L$with_cuda/lib64/stubs',
                          'configure.ac', string=True)
  
      def configure_args(self):
          args = []
  
          if '+cuda' in self.spec:
              args.append('--with-cuda=%s' % spec['cuda'].prefix)
          else:
              args.append('--without-cuda')
  
          return args
  
      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)
  
new_contents: # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class Libbeagle(AutotoolsPackage, CudaPackage):
      """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/v3.1.2.tar.gz"
  
      version('3.1.2', sha256='dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275')
      version('2.1.2', '1107614e86f652f8ee45c1c92f2af3d4',
              url='https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz')
  
      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 patch(self):
          # update cuda architecture if necessary
          if '+cuda' in self.spec:
              arch = self.spec.variants['cuda_arch'].value
              archflag = ''
  
              if arch[0] != 'none':
                  archflag = '-arch=%s' % arch[0]
  
              filter_file('-arch compute_13', archflag,
                          'libhmsbeagle/GPU/kernels/Makefile.am',
                          string=True)
  
              # point CUDA_LIBS to libcuda.so
              filter_file('-L$with_cuda/lib', '-L$with_cuda/lib64/stubs',
                          'configure.ac', string=True)
  
      def configure_args(self):
          args = []
  
          if '+cuda' in self.spec:
              args.append('--with-cuda=%s' % spec['cuda'].prefix)
          else:
              args.append('--without-cuda')
  
          return args
  
      def setup_environment(self, spack_env, run_env):
          prefix = self.prefix
          run_env.prepend_path('BEAST_LIB', prefix.lib)
  
subject: add 3.1.2 (#10789)