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 Trimmomatic(Package):
      """A flexible read trimming tool for Illumina NGS data."""
  
      homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
      url      = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
  
      # Older version aren't explicitly made available, but the URL
      # works as we'd like it to, so...
      version('0.39', sha256='2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca')
      version('0.38', sha256='d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c')
      version('0.36', sha256='4846c42347b663b9d6d3a8cef30da2aec89fc718bf291392c58e5afcea9f70fe')
      version('0.33', sha256='6968583a6c5854a44fff7d427e7ccdcb8dc17f4616082dd390a0633f87a09e3d')
  
      depends_on('java@8', type='run')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          jar_file = 'trimmomatic-{v}.jar'.format(v=self.version.dotted)
          install(jar_file, prefix.bin)
  
          # Put the adapter files someplace sensible
          install_tree('adapters', prefix.share.adapters)
  
          # Set up a helper script to call java on the jar file,
          # explicitly codes the path for java and the jar file.
          script_sh = join_path(os.path.dirname(__file__), "trimmomatic.sh")
          script = prefix.bin.trimmomatic
          install(script_sh, script)
          set_executable(script)
  
          # Munge the helper script to explicitly point to java and the
          # jar file.
          java = self.spec['java'].prefix.bin.java
          kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
          filter_file('^java', java, script, **kwargs)
          filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
                      script, **kwargs)
  