Merge branch 'master' of gitosis@mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / scripts / retrieve_config

diff --git a/scripts/retrieve_config b/scripts/retrieve_config
deleted file mode 100755 (executable)
index e4fdff1..0000000
--- a/scripts/retrieve_config
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/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:]))