def set_parser(parser): """Set up argument parser.""" parser.add_argument("root_dir", type=str, default=None, help="Root directory for ICE, " + \ "e.g., SMRTPortal data/clusterOutDir") parser = add_nfl_fa_arguments(parser, positional=True) parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True) parser = add_polished_isoforms_arguments(parser) parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser): """Set argument parser.""" parser.add_argument("root_dir", type=str, help="Root directory for ICE, " + "e.g., SMRTPortal data/clusterOutDir") parser = add_polished_isoforms_arguments(parser) parser.add_argument( "--use_sge", default=False, dest="use_sge", action="store_true", help="quiver jobs have been submitted to sge." "Check qstat", ) parser.add_argument( "--quit_if_not_done", default=False, dest="quit_if_not_done", action="store_true", help="Quit if quiver jobs haven't been completed.", )
def set_parser(parser): """Set argument parser.""" parser.add_argument("root_dir", type=str, help="Root directory for ICE, " + \ "e.g., SMRTPortal data/clusterOutDir") parser = add_polished_isoforms_arguments(parser) parser.add_argument("--use_sge", default=False, dest="use_sge", action="store_true", help="quiver jobs have been submitted to sge." "Check qstat") parser.add_argument("--quit_if_not_done", default=False, dest="quit_if_not_done", action="store_true", help="Quit if quiver jobs haven't been completed.")