5 from gaworkflow.pipeline.configure_run import *
6 from gaworkflow.pipeline import retrieve_config as _rc
7 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
9 s_fc = re.compile('FC[0-9]+')
11 #Turn on built-in command-line parsing.
12 _rc.DISABLE_CMDLINE = False
14 GENOME_DIR = '/data-store01/compbio/genomes/'
20 ci.analysis_dir = os.getcwd()
21 ci.base_analysis_dir, junk = os.path.split(ci.analysis_dir)
23 #FIXME: make a better command line tool
24 skip_retrieve_config = False
30 cfg_filepath = os.path.abspath('config32auto.txt')
32 #else, config file provide
34 cfg_filepath = os.path.abspath(args[0])
35 skip_retrieve_config = True
38 " configure_pipeline FC#####\n" \
40 " configure_pipeline <conf_filepath>\n"
43 genome_dir = GENOME_DIR
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"
50 print "Failed to retrieve config file"
52 print "Config file %s provided from command-line" % (cfg_filepath)
53 ci.config_filepath = cfg_filepath
54 status_retrieve_cfg = True
56 if status_retrieve_cfg:
57 status = configure(ci)
59 print "Configure success"
61 print "Configure failed"
63 print 'Run Dir:', ci.run_path
64 print 'Bustard Dir:', ci.bustard_path
67 # Setup status cmdline status monitor
68 startCmdLineStatusMonitor(ci)
70 print 'Running pipeline now!'
71 run_status = run_pipeline(ci)
72 if run_status is True:
73 print 'Pipeline ran successfully.'
76 print 'Pipeline run failed.'
81 if __name__ == "__main__":
82 sys.exit(main(sys.argv[1:]))