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

[htsworkflow.git] / scripts / htsw-get-config

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