run_jobs.py

#!/usr/bin/env python3

'''
Run jobs for loop-helix-loop reshaping. Before launching this 
wrapper script. you should write your costumized script the specify what
to do.
Then run your scripts with this wrapper.

Usage:
    ./run_jobs.py <name> <job-script> [options]

Arguments:
    <name>
        Name of the job.

    <job-script>
        Job script for the analysis.

Options:
    --job-distributor=<JD>, -d=<JD>  [default: sequential]
        Job distributor that runs the jobs.

    --hold-jid=<JID>, -h=<JID>  
        For SGEJobDistributor, hold the job until some jobs are finished.

    --keep-job-output-path, -k
        For SGEJobDistributor, do not clear the job output path.

    --job-script-arguments=<JA>, -a=<JA>  [default: ]
        Arguments passed to the job script. The job script will run
        as:
            job-script data-set-path job-script-arguments

    --num-jobs=<NJ>, -n=<NJ>
        Number of jobs for parallel run.
'''

import docopt

import loop_helix_loop_reshaping as LHLR


if __name__ == '__main__':

    arguments = docopt.docopt(__doc__)
    
    # Convert job-script arguments into a list
    
    job_script_arguments = arguments['--job-script-arguments'].split()
    
    # Initialize the job distributor and run the job
    
    job_distributor = None
    
    if arguments['--job-distributor'] == 'sequential':
        job_distributor = LHLR.job_distributors.SequentialJobDistributor(arguments['<name>'],
                          arguments['<job-script>'], job_script_arguments)
        
        job_distributor.run()
    
    elif arguments['--job-distributor'] == 'SGE':
        job_distributor = LHLR.job_distributors.SGEJobDistributor(arguments['<name>'],
                          arguments['<job-script>'], job_script_arguments)
    
        num_jobs = arguments['--num-jobs'] if arguments['--num-jobs'] else 1
    
        job_distributor.run(num_jobs, hold_jid=arguments['--hold-jid'], keep_job_output_path=arguments['--keep-job-output-path'])
    
    else:
        raise IOError('Unknown job distributor: {0}'.format(arguments['--job-distributor']))