Preps the metapipe main job to be submitted.

def make_submit_job(shell, output, job_type):
    """ Preps the metapipe main job to be submitted. """
    run_cmd = [shell, output]
    submit_command = Command(alias=PIPELINE_ALIAS, cmds=run_cmd)
    submit_job = get_job(submit_command, job_type)
    submit_job.make()
    return submit_job