create_job_histogram.py

import os, sys, datetime
"""
This needs module load python/2.6.5 in .bash_profile
"""
def create_job_file(sample):

    command = "Rscript /gpfs/home/gerikson/scripts/Wellderly_scripts/GitHub/Coverage_histogram.R"
    jobfile = jobs_folder + str(sample) + ".job"         
    outjob = open(jobfile, 'w')
    outjob.write("#!/bin/csh\n")                    
    outjob.write("#PBS -S /bin/bash\n")
    outjob.write("#PBS -l nodes=1:ppn=1\n")
    outjob.write("#PBS -l mem=24gb\n")
    outjob.write("#PBS -l walltime=500:00:00\n")
    outjob.write("#PBS -l cput=9600:00:00\n")
    outjob.write("#PBS -m n\n")
    outjob.write(command + "\n")
    outjob.close()  
    execute = QSUB + ' -e '+ jobs_folder + str(sample) + '.job.err -o ' + jobs_folder + str(sample)  + '.job.out ' + jobfile
    print execute 

    sys.stdout.flush()
    clustnum = os.popen(execute, 'r')
    jobnum = clustnum.readline().strip()
    clustnum.close()


print 'start'
print datetime.datetime.now().time()

counter = 0
QSUB = "qsub -q workq -M gerikson@scripps.edu -l mem=24G -l cput=9600:00:00 -l walltime=500:00:00 "
jobs_folder = "/gpfs/group/stsi/data/projects/wellderly/GenomeComb/jobfolder/hist_allData."


create_job_file("Total_coverage_hist")