Install additional tools we cannot distribute, updating local manifest.

def _install_toolplus(args):
    """Install additional tools we cannot distribute, updating local manifest.
    """
    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))