4 from htsworkflow.pipelines.retrieve_config import *
5 from htsworkflow.pipelines import retrieve_config
7 #Turn on built-in command-line parsing.
8 retrieve_config.DISABLE_CMDLINE = False
14 #Display help if no args are presented
15 options = getCombinedOptions(argv)
18 logging.basicConfig(level=logging.DEBUG)
20 logging.basicConfig(level=logging.INFO)
22 msg_list = ['ERROR MESSAGES:']
23 if options.flowcell is None:
24 msg_list.append(" Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
26 if options.url is None:
27 msg_list.append(" URL argument required (-u <url> or --url=<url>), or entry\n" \
28 " in /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
29 if options.genome_dir is None:
30 msg_list.append(" genome_dir argument required (-g <genome_dir> or \n" \
31 " --genome_dir=<genome_dir>, or entry in \n" \
32 " /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
35 print '\n'.join(msg_list)
38 saveConfigFile(options)
42 if __name__ == "__main__":
43 sys.exit(main(sys.argv[1:]))