Install a jar for GATK or associated tools like MuTect.

def _install_gatk_jar(name, fname, manifest, system_config, toolplus_dir):
    """Install a jar for GATK or associated tools like MuTect.
    """
    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)