code: def _install_toolplus(args):
      
      manifest_dir = os.path.join(_get_data_dir(), "manifest")
      toolplus_manifest = os.path.join(manifest_dir, "toolplus-packages.yaml")
      system_config = os.path.join(_get_data_dir(), "galaxy", "bcbio_system.yaml")
      # Handle toolplus installs inside Docker container
      if not os.path.exists(system_config):
          docker_system_config = os.path.join(_get_data_dir(), "config", "bcbio_system.yaml")
          if os.path.exists(docker_system_config):
              system_config = docker_system_config
      toolplus_dir = os.path.join(_get_data_dir(), "toolplus")
      for tool in args.toolplus:
          if tool.name in set(["gatk", "mutect"]):
              print("Installing %s" % tool.name)
              _install_gatk_jar(tool.name, tool.fname, toolplus_manifest, system_config, toolplus_dir)
          else:
              raise ValueError("Unexpected toolplus argument: %s %s" % (tool.name, tool.fname))
docs: Install additional tools we cannot distribute, updating local manifest.