2 from __future__ import print_function
5 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
6 os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
10 from htsworkflow.pipelines.retrieve_config import *
11 from htsworkflow.pipelines import retrieve_config
13 #Turn on built-in command-line parsing.
14 retrieve_config.DISABLE_CMDLINE = False
21 #Display help if no args are presented
22 options = getCombinedOptions(argv)
25 logging.basicConfig(level=logging.DEBUG)
27 logging.basicConfig(level=logging.INFO)
29 msg_list = ['ERROR MESSAGES:']
30 if options.flowcell is None:
32 " Flow cell argument required. -f <flowcell> or "\
33 "--flowcell=<flowcell>")
35 if options.url is None:
37 " URL argument required (-u <url> or --url=<url>), or entry\n" \
38 " in /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
40 if options.genome_dir is None:
42 " genome_dir argument required (-g <genome_dir> or \n" \
43 " --genome_dir=<genome_dir>, or entry in \n" \
44 " /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
47 print('\n'.join(msg_list))
50 saveConfigFile(options)
54 if __name__ == "__main__":
55 sys.exit(main(sys.argv[1:]))