Submitting BFAST via SAGA/Condor on OSG

bfast.saga.py

import saga

try:
  jd = saga.job.description()
  jd.set_attribute       ("Executable", "/home/oweidner/software/bfast/bin/bfast")
  jd.set_vector_attribute("Arguments", ["match", "-r", "reads.10.fastq", "-A", "1", "-f", "hg_2122.fa"])
  jd.set_attribute       ("Output", "my_out.$(Cluster).$(Process)")
  jd.set_attribute       ("Error", "my_err.$(Cluster).$(Process)")

  input_files = ["/home/oweidner/software/bfast/data/small/reference/hg_2122.fa > hg_2122.fa",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.10.1.bif > hg_2122.fa.cs.10.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.9.1.bif > hg_2122.fa.cs.9.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.8.1.bif > hg_2122.fa.cs.8.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.7.1.bif > hg_2122.fa.cs.7.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.6.1.bif > hg_2122.fa.cs.6.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.5.1.bif > hg_2122.fa.cs.5.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.4.1.bif > hg_2122.fa.cs.4.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.3.1.bif > hg_2122.fa.cs.3.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.2.1.bif > hg_2122.fa.cs.2.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.1.1.bif > hg_2122.fa.cs.1.1.bif",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.brg > hg_2122.fa.cs.brg",
  "/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.nt.brg > hg_2122.fa.nt.brg",
  "/home/oweidner/software/bfast/data/small/reads_5K/reads.10.fastq > reads.10.fastq"]

  jd.set_vector_attribute("FileTransfer", input_files)

  js = saga.job.service("condor://localhost")

  job = js.create_job(jd)
  job.run()

except saga.exception, e:
  print "ERROR: " 
  for err in e.get_all_messages():
    print err