toil_slurm_submit_multiple.py

#!/usr/bin/env python

from toil.job import Job

def fn(job, i):
    job.fileStore.logToMaster("Parent says: i is %s" % i, level=100)
    return i+1

def child_worker(job, i):
    job.fileStore.logToMaster("Child says: i is %s" % i, level=100)
    return i

def sum_it_all(job):
    job.fileStore.logToMaster("Merging results from all children", level=100)


if __name__=="__main__":
## Toil options
    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")
    options.batchSystem = 'slurm'
    options.logLevel = 'DEBUG'

    # Dummy parent job
    parent = Job.wrapJobFn(fn, 1)

    for child in xrange(1,5):
        parent.addChildJobFn(child_worker, child)

    wrapup = parent.addFollowOnJobFn(sum_it_all)
    
    Job.Runner.startToil(parent, options)