SGE script wrapper

wrapToSGE

#!/usr/bin/env python

import subprocess
import sys
import os
import time

#time_stamp=time.strftime("%y-%m-%d_%H-%M-%S")
time_stamp=str(time.time())

if len(sys.argv) < 2:
    sys.stderr.write("Need more parameters: <command> \"<all command options>\" \n")
    sys.exit()

main_name = sys.argv[1]

#argvs = []
#for p in sys.argv[2:]:
#    if os.path.isfile(p):
#        argvs.append( os.path.realpath(p))
#    else:
#        argvs.append(p)

#options = " ".join(argvs)
options = sys.argv[2]
cwd = os.getcwd()

job_name = main_name + "_" + time_stamp

sge_template = """#!/bin/bash
#$ -N %s
#$ -e /home/foobar/logs/  -o /home/foobar/logs/
#$ -S /bin/bash
#$ -M [email protected]

source /home/foobar/.bashrc

#mkdir -p -m 700 /scratch/foobar/job_%s

cd %s
%s %s &> %s%s.log
""" % (job_name,time_stamp,cwd,main_name,options,"sge_",job_name)

f = open("sge_"+time_stamp+".sh","w")

f.write( sge_template )

f.close()

subprocess.check_call(['qsub','sge_'+time_stamp+'.sh'])