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 import retrieve_config
   7 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
   8
   9 s_fc = re.compile('FC[0-9]+')
  10
  11 #Turn on built-in command-line parsing.
  12 retrieve_config.DISABLE_CMDLINE = False
  13
  14 GENOME_DIR = '/data-store01/compbio/genomes/'
  15
  16
  17
  18 def main(args=None):
  19   ci = ConfigInfo()
  20
  21   #FIXME: make a better command line tool
  22   skip_retrieve_config = False
  23   if len(args) == 1:
  24     arg = args[0]
  25
  26     #If FC##### found
  27     if s_fc.search(arg):
  28       cfg_filepath = os.path.abspath('config32auto.txt')
  29       flowcell = arg
  30     #else, config file provide
  31     else:
  32       cfg_filepath = os.path.abspath(args[0])
  33       skip_retrieve_config = True
  34   else:
  35     print "usage:\n" \
  36           "       configure_pipeline FC#####\n" \
  37           " or:\n" \
  38           "       configure_pipeline <conf_filepath>\n"
  39     return 3
  40
  41   genome_dir = GENOME_DIR
  42
  43   if not skip_retrieve_config:
  44     status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
  45     if status_retrieve_cfg:
  46       print "Retrieve config file successful"
  47     else:
  48       print "Failed to retrieve config file"
  49   else:
  50     print "Config file %s provided from command-line" % (cfg_filepath)
  51     ci.config_filepath = cfg_filepath
  52     status_retrieve_cfg = True
  53
  54   if status_retrieve_cfg:
  55     status = configure(ci)
  56     if status:
  57       print "Configure success"
  58     else:
  59       print "Configure failed"
  60
  61     print 'Run Dir:', ci.run_path
  62     print 'Bustard Dir:', ci.bustard_path
  63
  64     if status:
  65       # Setup status cmdline status monitor
  66       startCmdLineStatusMonitor(ci)
  67
  68       print 'Running pipeline now!'
  69       run_status = run_pipeline(ci)
  70       if run_status is True:
  71         print 'Pipeline ran successfully.'
  72         return 0
  73       else:
  74         print 'Pipeline run failed.'
  75         return 1
  76
  77     return 2
  78
  79 if __name__ == "__main__":
  80   sys.exit(main(sys.argv[1:]))