From: Diane Trout <diane@caltech.edu>
Date: Fri, 21 Oct 2011 18:37:02 +0000 (-0700)
Subject: Yes generate regular gerald config file.
X-Git-Tag: v0.5.5~83^2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=764cd85cb41444c196bcf01c8a58d74631a476a1

Yes generate regular gerald config file.
---

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 2292cb9..48b581e 100644
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -320,15 +320,15 @@ def saveConfigFile(options):
   genome_map = constructMapperDict(available_genomes)
   logging.debug('available genomes: %s' % ( unicode( genome_map.keys() ),))
 
-  #config = format_gerald_config(options, flowcell_info, genome_map)
-  #
-  #if options.output_filepath is not None:
-  #    outstream = open(options.output_filepath, 'w')
-  #    logging.info('Writing config file to %s' % (options.output_filepath,))
-  #else:
-  #    outstream = sys.stdout
-  #
-  #outstream.write(config)
+  config = format_gerald_config(options, flowcell_info, genome_map)
+
+  if options.output_filepath is not None:
+      outstream = open(options.output_filepath, 'w')
+      logging.info('Writing config file to %s' % (options.output_filepath,))
+  else:
+      outstream = sys.stdout
+
+  outstream.write(config)
 
   if options.sample_sheet is None:
       pass