code: def _install_gatk_jar(name, fname, manifest, system_config, toolplus_dir):
      
      if not fname.endswith(".jar"):
          raise ValueError("--toolplus argument for %s expects a jar file: %s" % (name, fname))
      version = get_gatk_jar_version(name, fname)
      store_dir = utils.safe_makedir(os.path.join(toolplus_dir, name, version))
      shutil.copyfile(fname, os.path.join(store_dir, os.path.basename(fname)))
      _update_system_file(system_config, name, {"dir": store_dir})
      _update_manifest(manifest, name, version)
docs: Install a jar for GATK or associated tools like MuTect.