text: # 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 *
  import os
  
  
  class Blasr(Package):
      """The PacBio long read aligner."""
  
      homepage = "https://github.com/PacificBiosciences/blasr/wiki"
      url      = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
  
      version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a')
  
      depends_on('ncurses')
      depends_on('hdf5+cxx@1.8.12:1.8.99')
      depends_on('htslib')
      depends_on('zlib')
      depends_on('boost')
      depends_on('pbbam')
      depends_on('blasr-libcpp')
      depends_on('python', type='build')
  
      phases = ['configure', 'build', 'install']
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PATH', self.spec.prefix.utils)
          spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
          spack_env.prepend_path('CPATH', self.spec[
                                 'blasr-libcpp'].prefix.pbdata)
          spack_env.prepend_path('CPATH', self.spec[
                                 'blasr-libcpp'].prefix.alignment)
          spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
  
          # hdf has +mpi by default, so handle that possibility
          if ('+mpi' in self.spec['hdf5']):
              spack_env.set('CC', self.spec['mpi'].mpicc)
              spack_env.set('CXX', self.spec['mpi'].mpicxx)
  
      def configure(self, spec, prefix):
          configure_args = [
              'LIBPBDATA_INC={0}'.format(
                  self.spec['blasr-libcpp'].prefix),
              'LIBPBDATA_LIB={0}'.format(
                  self.spec['blasr-libcpp'].prefix.pbdata),
              'LIBBLASR_LIB={0}'.format(
                  self.spec['blasr-libcpp'].prefix.alignment),
              'LIBBLASR_INC={0}'.format(
                  self.spec['blasr-libcpp'].prefix),
              'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
              'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
              'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
              'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
              '--shared'
          ]
          python('configure.py', *configure_args)
  
      def build(self, spec, prefix):
          os.environ['CPLUS_INCLUDE_PATH'] = join_path(
              self.stage.source_path, 'include')
          make()
  
      def install(self, spec, prefix):
          mkdir(prefix.utils)
          mkdir(prefix.bin)
          install('blasr', prefix.bin.blasr)
          install('utils/loadPulses', prefix.utils)
          install('utils/pls2fasta', prefix.utils)
          install('utils/samFilter', prefix.utils)
          install('utils/samtoh5', prefix.utils)
          install('utils/samtom4', prefix.utils)
          install('utils/sawriter', prefix.utils)
          install('utils/sdpMatcher', prefix.utils)
          install('utils/toAfg', prefix.utils)
  