main.py

#!/usr/bin/python


def get_args():
    """
    get user defined arguments.
    """

    try:
        import argparse

        parser = argparse.ArgumentParser(description="parse arguments")
        parser.add_argument(
            "--docker", action="store_true", default=False, help="docker installation"
        )
        parser.add_argument(
            "--config",
            type=str,
            required=False,
            default="config.py",
            help="docker installation",
        )
        parser.add_argument(
            "--test",
            action="store_true",
            default=False,
            help="test software installation",
        )

        parser.add_argument(
            "--envs",
            action="store_true",
            default=False,
            help="Install software environments",
        )

        parser.add_argument(
            "--setup_conda",
            action="store_true",
            default=False,
            help="Install software conda environments",
        )

        parser.add_argument(
            "--seqdl",
            action="store_true",
            default=False,
            help="download sequence databases",
        )
        parser.add_argument(
            "--soft",
            action="store_true",
            default=False,
            help="Install software databases",
        )

        parser.add_argument(
            "--deploy",
            action="store_true",
            default=False,
            help="setup software deployment",
        )

        parser.add_argument(
            "--partial",
            action="store_true",
            default=False,
            help="Install software databases",
        )

        args = parser.parse_args()

    except TypeError as e:
        print("check report args")
        print(e)

    return args


def main():
    from install_scripts.install_source import ENVS_PARAMS, INSTALL_PARAMS

    CWD = os.getcwd()
    args = get_args()
    ###
    if not args.partial:
        args.setup_conda = True
        args.envs = True
        args.soft = True
        args.seqdl = True

        """     if args.docker:
                SOURCE = "/opt/conda/etc/profile.d/conda.sh"
                HOME = "/televir/mngs_benchmark/"
                ENVDIR = "/televir/mngs_benchmark/mngs_environments/"
                TECH = "nanopore"
                TAXDUMP = "/opt/taxdump.tar.gz"
                UPDATE = False

                ORGANISM = "viral"
                INSTALL_TYPE = "docker"

                INSTALL_PARAMS["HOME"] = HOME
                INSTALL_PARAMS["ENVSDIR"]["SOURCE"] = SOURCE
                INSTALL_PARAMS["ENVSDIR"]["ROOT"] = ENVDIR

                ENVS_PARAMS["SOURCE"] = SOURCE
                ENVS_PARAMS["ENVSDIR"] = ENVDIR
                ENVS_PARAMS["YMLDIR"] = CWD + "/install_scripts/yaml/"

            else: """

    try:
        mainconf = __import__(os.path.splitext(args.config)[0])
    except ImportError as e:
        logging.info(f"failed to import config file {args.config}")
        sys.exit(1)

    ENVDIR = mainconf.ENVDIR
    HOME = mainconf.HOME
    SOURCE = mainconf.SOURCE
    TAXDUMP = mainconf.TAXDUMP
    UPDATE = mainconf.UPDATE

    TECH = "nanopore"
    ORGANISM = "viral"
    INSTALL_TYPE = "docker"

    INSTALL_PARAMS["HOME"] = HOME
    INSTALL_PARAMS["ENVSDIR"]["SOURCE"] = SOURCE
    INSTALL_PARAMS["ENVSDIR"]["ROOT"] = ENVDIR

    ENVS_PARAMS["SOURCE"] = SOURCE
    ENVS_PARAMS["ENVSDIR"] = ENVDIR
    ENVS_PARAMS["YMLDIR"] = CWD + "/install_scripts/yaml/"

    ###
    from install_scripts.main_install import main_setup
    from install_scripts.modules.db_install import setup_dl, setup_install
    from install_scripts.modules.env_install import env_install
    from install_scripts.modules.utility_manager import Utility_Repository

    ####
    utility_repository = Utility_Repository(
        db_path=HOME, install_type=INSTALL_TYPE, file_prefix="utility"
    )

    env_manager = env_install(ENVS_PARAMS)

    dl_manager = setup_dl(INSTALL_PARAMS, update=UPDATE)

    install_manager = setup_install(
        INSTALL_PARAMS,
        taxdump=TAXDUMP,
        test=args.test,
        update=UPDATE,
    )

    metagen_prep = main_setup(
        env_manager,
        dl_manager,
        install_manager,
        utility_repository,
        ENVS_PARAMS=ENVS_PARAMS,
        INSTALL_PARAMS=INSTALL_PARAMS,
        pdir=CWD + "/install_scripts/",
    )

    metagen_prep.object_input(
        envs=args.envs,
        seqdl=args.seqdl,
        soft=args.soft,
        nanopore=(TECH == "nanopore"),
        taxdump=TAXDUMP,
        organism=ORGANISM,
        test=args.test,
    )

    if args.setup_conda:
        metagen_prep.setup_envs_conda()

    if args.envs:
        metagen_prep.setup_envs()

    os.system(
        f"cp install_scripts/bin/* {ENVDIR + INSTALL_PARAMS['ENVSDIR']['centrifuge']}/bin/"
    )

    metagen_prep.setup_dir()

    if metagen_prep.seqdl or metagen_prep.soft:
        os.system(f"cp install_scripts/metadata/* {metagen_prep.wdir.metadir}")

    metagen_prep.setup_soft()
    ############
    ############


if __name__ == "__main__":
    import logging
    import os
    import sys

    logging.basicConfig(
        format="%(asctime)s - %(message)s",
        datefmt="%d-%b-%y %H:%M:%S",
        level=logging.INFO,
    )
    main()