def add_ice_quiver_all_arguments(parser): """Add arguments for IceQuiverAll, including arguments for IceQuiver and IceQuiverPostprocess.""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True) parser = add_cluster_summary_report_arguments(parser) parser = add_ice_post_quiver_hq_lq_arguments(parser) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True) return parser
def add_ice_quiver_postprocess_arguments(parser): """Add arugments for IceQuiverPostprocess (ice_quiver.py postprocess).""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_ice_post_quiver_hq_lq_arguments(parser) parser = add_cluster_summary_report_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.") return parser