#!/usr/bin/env python
+import logging
import sys
-from gaworkflow.pipeline.retrieve_config import *
+from htsworkflow.pipelines.retrieve_config import *
+from htsworkflow.pipelines import retrieve_config
-def main(args=None):
- #Display help if no args are presented
- if len(sys.argv) == 1:
- sys.argv.append('-h')
+#Turn on built-in command-line parsing.
+retrieve_config.DISABLE_CMDLINE = False
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
- options = getCombinedOptions()
+ #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.output_filepath is None:
- msg_list.append(" Output filepath argument required. -o <filepath> or --output=<filepath>")
-
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.flowcell, options.url, options.output_filepath)
+ saveConfigFile(options)
+
return 0
if __name__ == "__main__":