def main(argv=sys.argv): return pacbio_args_runner( argv=argv[1:], parser=get_parser(), args_runner_func=args_runner, alog=log, setup_log_func=setup_log)
def main(argv=sys.argv, out=sys.stdout): setup_log_ = functools.partial( setup_log, str_formatter='%(asctime)s [%(levelname)s] %(message)s') try: return pacbio_args_runner(argv=argv[1:], parser=get_parser(), args_runner_func=args_runner, alog=logging.getLogger(__name__), setup_log_func=setup_log) # FIXME is there a more central place to deal with this? except Exception as e: type, value, tb = sys.exc_info() traceback.print_exc(file=sys.stderr) # Note: if kt.args.usePdb # This won't work. If an exception is raised in parseArgs, # then kt.args is not defined yet. if '--pdb' in argv: try: # this has better integration with ipython and is nicer # pip install ipdb import ipdb ipdb.post_mortem(tb) except ImportError: import pdb pdb.post_mortem(tb) else: # exit non-zero raise
def main(argv=sys.argv[1:]): """Main point of Entry""" return pacbio_args_runner(argv=argv, parser=get_parser(), args_runner_func=args_runner, alog=log, setup_log_func=setup_log)
def main(argv=sys.argv): parser = get_parser() return pacbio_args_runner(argv[1:], parser, _args_run_butler, log, setup_log_func=None)
def main(argv=sys.argv[1:]): """Main point of Entry""" return pacbio_args_runner( argv=argv, parser=get_parser(), args_runner_func=args_runner, alog=log, setup_log_func=setup_log)
def main(argv=sys.argv): parser = get_parser() # note, this logger will overwritten after the output dir is created return pacbio_args_runner(argv[1:], parser, _args_run_butler, log, setup_log_func=setup_log)
def main(argv=sys.argv): setup_log_ = functools.partial( setup_log, str_formatter='%(asctime)s [%(levelname)s] %(message)s') return pacbio_args_runner(argv=argv[1:], parser=get_parser(), args_runner_func=args_runner, alog=logging.getLogger(__name__), setup_log_func=setup_log_)
def main(argv=sys.argv): parser = get_parser() return pacbio_args_runner(argv[1:], parser, _args_run_butler, log, setup_minimal_log)
def _main(argv=sys.argv): return pacbio_args_runner(argv[1:], _get_parser(), _registry_runner(registry), log, setup_log)
def main(argv=None): argv_ = sys.argv if argv is None else argv parser = get_parser() return pacbio_args_runner(argv_[1:], parser, _args_run_multi_testkit_cfg, log, setup_log)
def main(argv=sys.argv): parser = get_parser() return pacbio_args_runner(argv[1:], parser, convert_pipeline_json_files_args, log, setup_log)
def main(argv): return pacbio_args_runner(argv[1:], _get_parser(), run_args, log, setup_log_func=setup_log)
def main(argv=sys.argv): return pacbio_args_runner( argv[1:], get_parser_impl(Constants), functools.partial(run_args_impl, run_bam_to_fastq), log, setup_log)
def main(argv=sys.argv): return pacbio_args_runner(argv[1:], get_parser(), args_runner, log, setup_log)
def main(argv=sys.argv): return pacbio_args_runner(argv=argv[1:], parser=get_parser(), args_runner_func=run_args, alog=logging.getLogger(), setup_log_func=setup_log)
def main(argv): return pacbio_args_runner(argv[1:], get_parser(), args_runner, log, setup_log_func=setup_log)
def main(argv=None): argv_ = sys.argv if argv is None else argv parser = get_parser() return pacbio_args_runner(argv_[1:], parser, _args_to_render_report, log, setup_log)
def main(argv=sys.argv): logging.basicConfig(level=logging.DEBUG) log = logging.getLogger() return pacbio_args_runner(argv[1:], get_parser(), args_runner, log, setup_log)