5 from gaworkflow.pipeline.configure_run import *
6 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
8 s_fc = re.compile('FC[0-9]+')
11 GENOME_DIR = '/data-store01/compbio/genomes/'
18 #FIXME: make a better command line tool
19 skip_retrieve_config = False
25 cfg_filepath = os.path.abspath('config32auto.txt')
27 #else, config file provide
29 cfg_filepath = os.path.abspath(args[0])
30 skip_retrieve_config = True
33 " configure_pipeline FC#####\n" \
35 " configure_pipeline <conf_filepath>\n"
38 genome_dir = GENOME_DIR
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"
45 print "Failed to retrieve config file"
47 print "Config file %s provided from command-line" % (cfg_filepath)
48 ci.config_filepath = cfg_filepath
49 status_retrieve_cfg = True
51 if status_retrieve_cfg:
52 status = configure(ci)
54 print "Configure success"
56 print "Configure failed"
58 print 'Run Dir:', ci.run_path
59 print 'Bustard Dir:', ci.bustard_path
62 # Setup status cmdline status monitor
63 startCmdLineStatusMonitor(ci)
65 print 'Running pipeline now!'
66 run_status = run_pipeline(ci)
67 if run_status is True:
68 print 'Pipeline ran successfully.'
71 print 'Pipeline run failed.'
76 if __name__ == "__main__":
77 sys.exit(main(sys.argv[1:]))