Add the option to copy tree in addition to making a symlink tree from elsewhere.

[htsworkflow.git] / encode_submission / trackhub.py

diff --git a/encode_submission/trackhub.py b/encode_submission/trackhub.py
index 41f76d14f6d552f5a25eb0ee1bc74f9db32e18c6..4fea5cc827eca6ef7aa08c39642e6bd4aa1dac0b 100644 (file)
--- a/encode_submission/trackhub.py
+++ b/encode_submission/trackhub.py
@@ -27,7 +27,6 @@ import RDF
 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, \
@@ -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")