Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4

diff --combined encode_submission/trackhub.py
index 4fea5cc827eca6ef7aa08c39642e6bd4aa1dac0b,c5c254358f972289bba132deae366c9dbcc897f9..fb0cea8771dcbc25b11dc95654e1e12ed62d2eb9
--- 1/encode_submission/trackhub.py
--- 2/encode_submission/trackhub.py
+++ b/encode_submission/trackhub.py
@@@ -27,6 -27,7 +27,6 @@@ import RD
  if not 'DJANGO_SETTINGS_MODULE' in os.environ:
      os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
  
 -
  from htsworkflow.util import api
  from htsworkflow.util.rdfhelp import \
       dafTermOntology, \
@@@ -77,10 -78,10 +77,10 @@@ def main(cmdline=None)
              logger.warn("File %s doesn't exist.", a)
  
      if opts.make_link_tree_from is not None:
 -        results.make_tree_from(opts.make_tree_from, link=True)
 +        results.make_tree_from(opts.make_link_tree_from, link=True)
  
      if opts.copy_tree_from is not None:
 -        results.make_tree_from(opts.make_tree_from, link=False)
 +        results.make_tree_from(opts.copy_tree_from, link=False)
  
      if opts.fastq:
          logger.info("Building fastq extraction scripts")
@@@ -96,7 -97,7 +96,7 @@@
          mapper.scan_submission_dirs(results)
  
      if opts.make_hub:
-         mapper.make_hub(results)
+         make_hub(results)
  
      if opts.sparql:
          sparql_query(model, opts.sparql)
@@@ -106,6 -107,18 +106,18 @@@
          print writer.serialize_model_to_string(model)
  
  
+ def make_hub(results):
+     trackdb = mapper.make_hub(results)
+     manifest = mapper.make_manifest(results)
+ 
+     trackstream = sys.stdout
+     #with open('trackDb.txt', 'w') as trackstream:
+     trackstream.write(trackdb)
+ 
+     #with open('manifest.txt', 'w') as mainifeststream:
+     manifeststream = sys.stdout
+     mainifeststream.write(mainifest)
+         
  def make_parser():
      parser = OptionParser()