5 from gaworkflow.pipeline.configure_run import *
6 from gaworkflow.pipeline import retrieve_config
7 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
9 s_fc = re.compile('FC[0-9]+')
11 #Turn on built-in command-line parsing.
12 retrieve_config.DISABLE_CMDLINE = False
14 GENOME_DIR = '/data-store01/compbio/genomes/'
21 #FIXME: make a better command line tool
22 skip_retrieve_config = False
28 cfg_filepath = os.path.abspath('config32auto.txt')
30 #else, config file provide
32 cfg_filepath = os.path.abspath(args[0])
33 skip_retrieve_config = True
36 " configure_pipeline FC#####\n" \
38 " configure_pipeline <conf_filepath>\n"
41 genome_dir = GENOME_DIR
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"
48 print "Failed to retrieve config file"
50 print "Config file %s provided from command-line" % (cfg_filepath)
51 ci.config_filepath = cfg_filepath
52 status_retrieve_cfg = True
54 if status_retrieve_cfg:
55 status = configure(ci)
57 print "Configure success"
59 print "Configure failed"
61 print 'Run Dir:', ci.run_path
62 print 'Bustard Dir:', ci.bustard_path
65 # Setup status cmdline status monitor
66 startCmdLineStatusMonitor(ci)
68 print 'Running pipeline now!'
69 run_status = run_pipeline(ci)
70 if run_status is True:
71 print 'Pipeline ran successfully.'
74 print 'Pipeline run failed.'
79 if __name__ == "__main__":
80 sys.exit(main(sys.argv[1:]))