Run simple script with python-cluster

run_rename.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Submit a bunch of jobs."""
import sys
import argparse
from time import sleep
import cluster


CMD = '/home/dacre/mike_tools/bin/rename_mesh_snps.py {bed} -i {infile} -o {outfile}'

def submit_files(bedfile, infiles):
    """Submit all infiles.

    :bedfile: The bed file of peak locations.
    :infiles: List of split files.

    """
    for sfile in infiles:
        job = cluster.submit(CMD.format(bed=bedfile, infile=sfile,
                                        outfile=sfile+'.out'),
                             mem=8000, name=sfile)
        sleep(1)
        print('Submitted {}'.format(job))


def main(argv=None):
    """Command line parsing."""
    if not argv:
        argv = sys.argv[1:]

    parser  = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter)

    # Positional arguments
    parser.add_argument('bedfile', help="Bedfile")
    parser.add_argument('infiles', nargs='+', help="Split files")

    args = parser.parse_args(argv)

    submit_files(args.bedfile, args.infiles)

if __name__ == '__main__' and '__file__' in globals():
    sys.exit(main())