-#!/usr/bin/env python
-import logging
-import sys
-from htsworkflow.pipelines.retrieve_config import *
-from htsworkflow.pipelines import retrieve_config
-
-#Turn on built-in command-line parsing.
-retrieve_config.DISABLE_CMDLINE = False
-
-def main(argv=None):
- if argv is None:
- argv = sys.argv
-
- #Display help if no args are presented
- options = getCombinedOptions(argv)
-
- if options.verbose:
- logging.basicConfig(level=logging.DEBUG)
- else:
- logging.basicConfig(level=logging.INFO)
-
- msg_list = ['ERROR MESSAGES:']
- if options.flowcell is None:
- msg_list.append(" Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
-
- if options.url is None:
- msg_list.append(" URL argument required (-u <url> or --url=<url>), or entry\n" \
- " in /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
- if options.genome_dir is None:
- msg_list.append(" genome_dir argument required (-g <genome_dir> or \n" \
- " --genome_dir=<genome_dir>, or entry in \n" \
- " /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
-
- if len(msg_list) > 1:
- print '\n'.join(msg_list)
- return 1
-
- saveConfigFile(options)
-
- return 0
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[1:]))