--- /dev/null
+#!/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:]))