3 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
4 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
8 from htsworkflow.pipelines.retrieve_config import *
9 from htsworkflow.pipelines import retrieve_config
11 #Turn on built-in command-line parsing.
12 retrieve_config.DISABLE_CMDLINE = False
19 #Display help if no args are presented
20 options = getCombinedOptions(argv)
23 logging.basicConfig(level=logging.DEBUG)
25 logging.basicConfig(level=logging.INFO)
27 msg_list = ['ERROR MESSAGES:']
28 if options.flowcell is None:
30 " Flow cell argument required. -f <flowcell> or "\
31 "--flowcell=<flowcell>")
33 if options.url is None:
35 " URL argument required (-u <url> or --url=<url>), or entry\n" \
36 " in /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
38 if options.genome_dir is None:
40 " genome_dir argument required (-g <genome_dir> or \n" \
41 " --genome_dir=<genome_dir>, or entry in \n" \
42 " /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
45 print '\n'.join(msg_list)
48 saveConfigFile(options)
52 if __name__ == "__main__":
53 sys.exit(main(sys.argv[1:]))