text: # Copyright 2013-2020 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.path
  
  
  class Snpeff(Package):
      """SnpEff is a variant annotation and effect prediction tool. It
      annotates and predicts the effects of genetic variants (such as
      amino acid changes)."""
  
      homepage = "http://snpeff.sourceforge.net/"
      url      = "https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
  
      version('2017-11-24', sha256='d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244')
  
      depends_on('jdk', type=('build', 'run'))
  
      def install(self, spec, prefix):
          install_tree('snpEff', prefix.bin)
  
          # Set up a helper script to call java on the jar files,
          # explicitly codes the path for java and the jar files.
          scripts = ['snpEff', 'SnpSift']
  
          for script in scripts:
              script_sh = join_path(os.path.dirname(__file__), script + ".sh")
              script_path = join_path(prefix.bin, script)
              install(script_sh, script_path)
              set_executable(script_path)
  
              # Munge the helper script to explicitly point to java and the
              # jar file.
              java = self.spec['java'].prefix.bin.java
              kwargs = {'backup': False}
              filter_file('^java', java, script_path, **kwargs)
              filter_file(script + '.jar',
                          join_path(prefix.bin, script + '.jar'),
                          script_path, **kwargs)
  