comparison data_manager_fetch_mapseq_db.py @ 1:4cd97cc67061 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 373300c0508fc239fa6d1c8a0351fa9cbb9c0426

0:dbf2735e8480

}

DB_names = {
    "mgnify_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
    "mgnify_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
    "mgnify_its_unite": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
    "mgnify_its_itsonedb": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
    "test_lsu": "Trimmed LSU Test DB",
}


def download_untar_store(url, tmp_path, dest_path):
    """
    Download a tar.gz file containing one folder,
    extract that folder and move the content inside dest_path 
    """

    extract_path = os.path.join(tmp_path, "extract")

    os.makedirs(tmp_path, exist_ok=True)

            folder_path = os.path.join(extract_path, folder)

            print(f"Copy data to {dest_path}")
            shutil.copytree(folder_path, dest_path)
            print("Done !")
    
    shutil.rmtree(tmp_path)


def main():
    # Parse Command Line

    # output paths
    db_path = os.path.join(workdir, db_value)
    tmp_path = os.path.join(workdir, "tmp")

    # create DB
    if args.test:  
        url = DB_paths["test_lsu"]
    else:
        url = DB_paths[args.db_type]

    # download data

1:4cd97cc67061

}

DB_names = {
    "mgnify_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
    "mgnify_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
    "mgnify_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
    "mgnify_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
    "test_lsu": "Trimmed LSU Test DB",
}


def download_untar_store(url, tmp_path, dest_path):
    """
    Download a tar.gz file containing one folder,
    extract that folder and move the content inside dest_path
    """

    extract_path = os.path.join(tmp_path, "extract")

    os.makedirs(tmp_path, exist_ok=True)

            folder_path = os.path.join(extract_path, folder)

            print(f"Copy data to {dest_path}")
            shutil.copytree(folder_path, dest_path)
            print("Done !")

    shutil.rmtree(tmp_path)


def main():
    # Parse Command Line

    # output paths
    db_path = os.path.join(workdir, db_value)
    tmp_path = os.path.join(workdir, "tmp")

    # create DB
    if args.test:
        url = DB_paths["test_lsu"]
    else:
        url = DB_paths[args.db_type]

    # download data