# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2016-2019
# (c) University of Strathclyde 2019-2020
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G4 0RE
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2016-2019 The James Hutton Institute
# Copyright (c) 2019-2020 University of Strathclyde
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# THE SOFTWARE.
"""Provides parser for arguments common to job scheduling."""
from argparse import ArgumentParser
[docs]def build() -> ArgumentParser:
"""Return the common argument parser for job scheduling.
:param subps: collection of subparsers in main parser
:param parents: parsers from which arguments are inherited
Common arguments are:
"""
parser = ArgumentParser(add_help=False)
parser.add_argument(
"--scheduler",
dest="scheduler",
action="store",
default="multiprocessing",
choices=["multiprocessing", "SGE"],
help="Job scheduler (default multiprocessing, " + "i.e. locally)",
)
parser.add_argument(
"--workers",
dest="workers",
action="store",
default=None,
type=int,
help="Number of worker processes for multiprocessing "
"(default zero, meaning use all available cores)",
)
parser.add_argument(
"--SGEgroupsize",
dest="sgegroupsize",
action="store",
default=10000,
type=int,
help="Number of jobs to place in an SGE array group " "(default 10000)",
)
parser.add_argument(
"--SGEargs",
dest="sgeargs",
action="store",
default=None,
type=str,
help="Additional arguments for qsub",
)
parser.add_argument(
"--jobprefix",
dest="jobprefix",
action="store",
default="PYANI",
help="Prefix for SGE jobs (default PYANI).",
)
return parser