def main(): """ The main function Runs the selection pipeline. """ args = parse_arguments() config = parse_config(args) set_environment(config['environment']) logging.basicConfig(format='%(levelname)s %(asctime)s %(message)s', filename=args.log_file, filemode='w', level=args.level) check_paths(config) try: cores = int(config['system']['cores_avaliable']) except: logging.error("Could not read cores_avaliable from the config file") # TODO - add real error messages sys.exit(1) logging.info("Creating Job Queue") job_queue = JobQueue(cores) logging.info("Success") ngadnap_graph = CreateNGaDNAPGraph(args=args, config=config, job_queue=job_queue) job_queue.set_command_graph(ngadnap_graph.command_graph) ngadnap_graph.populate() ngadnap_graph.run() print("NGaDNAP ran successfully")
def test_check_paths_simple(self): config = self._get_config() check_paths(config)