old_contents: from gscripts import qtools
  
  
  import pandas as pd
  
  import sys
  sInfo = pd.read_table(sys.argv[1])
  
  cmds = []
  
  Sub = qtools.Submitter()
  for row, dat in sInfo.iterrows():
      id =  dat['Sample ID']
      bam = dat['Bam File']
      out = id + ".splices"
      oldsplice_command = "oldsplice.py -b %s -s hg19 -o %s --splice_type SE --splice_type MXE --processors 16" %(bam, out)
      cmds.append(oldsplice_command)
      oldsplice_command = "oldsplice.py -f -b %s -s hg19 -o %s --splice_type SE --splice_type MXE --processors 16" %(bam, out.replace(".splices", ".flip.splices")  )
      cmds.append(oldsplice_command)
  Sub.job(command_list=cmds, sh_file="runOldsplice.sh", job_name="oldsplice", array=True, queue="home", nodes=1, ppn=16, submit=True)
  
new_contents: from gscripts import qtools
  
  
  import pandas as pd
  
  import sys
  sInfo = pd.read_table(sys.argv[1])
  
  cmds = []
  
  Sub = qtools.Submitter()
  for row, dat in sInfo.iterrows():
      id =  dat['Sample ID']
      bam = dat['Bam File']
      out = id + ".splices"
      oldsplice_command = "oldsplice.py -b %s -s hg19 -o %s --splice_type SE --splice_type MXE --processors 16" %(bam, out)
      cmds.append(oldsplice_command)
      oldsplice_command = "oldsplice.py -f -b %s -s hg19 -o %s --splice_type SE --splice_type MXE --processors 16" %(bam, out.replace(".splices", ".flip.splices")  )
      cmds.append(oldsplice_command)
  Sub.job(command_list=cmds, sh_file="runOldsplice.sh", job_name="oldsplice", array=True, queue="home", nodes=1, ppn=16, submit=True, max_running=1000)
  
subject: update qtools submitter call in submit_oldsplice.py with max_running