scripts/configure_pipeline

   1 #!/usr/bin/env python
   2 import os
   3 import sys
   4 import re
   5 from htsworkflow.pipelines.configure_run import *
   6 from htsworkflow.pipelines import retrieve_config as _rc
   7 from htsworkflow.pipelines.run_status import startCmdLineStatusMonitor
   8
   9 s_fc = re.compile('FC[0-9]+')
  10
  11 #Turn on built-in command-line parsing.
  12 _rc.DISABLE_CMDLINE = False
  13
  14 GENOME_DIR = '/data-store01/compbio/genomes/'
  15
  16
  17
  18 def main(args=None):
  19   ci = ConfigInfo()
  20   ci.analysis_dir = os.getcwd()
  21   ci.base_analysis_dir, junk = os.path.split(ci.analysis_dir)
  22
  23   #FIXME: make a better command line tool
  24   skip_retrieve_config = False
  25   if len(args) == 1:
  26     arg = args[0]
  27
  28     #If FC##### found
  29     if s_fc.search(arg):
  30       cfg_filepath = os.path.abspath('config32auto.txt')
  31       flowcell = arg
  32     #else, config file provide
  33     else:
  34       cfg_filepath = os.path.abspath(args[0])
  35       skip_retrieve_config = True
  36   else:
  37     print "usage:\n" \
  38           "       configure_pipeline FC#####\n" \
  39           " or:\n" \
  40           "       configure_pipeline <conf_filepath>\n"
  41     return 3
  42
  43   genome_dir = GENOME_DIR
  44
  45   if not skip_retrieve_config:
  46     status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
  47     if status_retrieve_cfg:
  48       print "Retrieve config file successful"
  49     else:
  50       print "Failed to retrieve config file"
  51   else:
  52     print "Config file %s provided from command-line" % (cfg_filepath)
  53     ci.config_filepath = cfg_filepath
  54     status_retrieve_cfg = True
  55
  56   if status_retrieve_cfg:
  57     status = configure(ci)
  58     if status:
  59       print "Configure success"
  60     else:
  61       print "Configure failed"
  62
  63     print 'Run Dir:', ci.run_path
  64     print 'Bustard Dir:', ci.bustard_path
  65
  66     if status:
  67       # Setup status cmdline status monitor
  68       startCmdLineStatusMonitor(ci)
  69
  70       print 'Running pipeline now!'
  71       run_status = run_pipeline(ci)
  72       if run_status is True:
  73         print 'Pipeline ran successfully.'
  74         return 0
  75       else:
  76         print 'Pipeline run failed.'
  77         return 1
  78
  79     return 2
  80
  81 if __name__ == "__main__":
  82   logging.basicConfig(level=logging.DEBUG,
  83                     format='%(asctime)s %(levelname)-8s %(message)s',
  84                     datefmt='%a, %d %b %Y %H:%M:%S',
  85                     #filename='pipeline_main.log',
  86                     filemode='w')
  87
  88   sys.exit(main(sys.argv[1:]))