scripts/configure_pipeline

   1 #!/usr/bin/env python
   2 import os
   3 import sys
   4 import re
   5 from gaworkflow.pipeline.configure_run import *
   6 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
   7
   8 s_fc = re.compile('FC[0-9]+')
   9
  10
  11 GENOME_DIR = '/data-store01/compbio/genomes/'
  12
  13
  14
  15 def main(args=None):
  16   ci = ConfigInfo()
  17
  18   #FIXME: make a better command line tool
  19   skip_retrieve_config = False
  20   if len(args) == 1:
  21     arg = args[0]
  22
  23     #If FC##### found
  24     if s_fc.search(arg):
  25       cfg_filepath = os.path.abspath('config32auto.txt')
  26       flowcell = arg
  27     #else, config file provide
  28     else:
  29       cfg_filepath = os.path.abspath(args[0])
  30       skip_retrieve_config = True
  31   else:
  32     print "usage:\n" \
  33           "       configure_pipeline FC#####\n" \
  34           " or:\n" \
  35           "       configure_pipeline <conf_filepath>\n"
  36     return 3
  37
  38   genome_dir = GENOME_DIR
  39
  40   if not skip_retrieve_config:
  41     status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
  42     if status_retrieve_cfg:
  43       print "Retrieve config file successful"
  44     else:
  45       print "Failed to retrieve config file"
  46   else:
  47     print "Config file %s provided from command-line" % (cfg_filepath)
  48     ci.config_filepath = cfg_filepath
  49     status_retrieve_cfg = True
  50
  51   if status_retrieve_cfg:
  52     status = configure(ci)
  53     if status:
  54       print "Configure success"
  55     else:
  56       print "Configure failed"
  57
  58     print 'Run Dir:', ci.run_path
  59     print 'Bustard Dir:', ci.bustard_path
  60
  61     if status:
  62       # Setup status cmdline status monitor
  63       startCmdLineStatusMonitor(ci)
  64
  65       print 'Running pipeline now!'
  66       run_status = run_pipeline(ci)
  67       if run_status is True:
  68         print 'Pipeline ran successfully.'
  69         return 0
  70       else:
  71         print 'Pipeline run failed.'
  72         return 1
  73
  74     return 2
  75
  76 if __name__ == "__main__":
  77   sys.exit(main(sys.argv[1:]))