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 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.")
