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