diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 153c4f53f9f..312a82e0b39 100755
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -847,11 +847,17 @@ class MoveDirectoryFiles( RecipeStep ):
 
     def move_directory_files( self, current_dir, source_dir, destination_dir ):
         source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) )
-        destination_directory = os.path.join( destination_dir )
-        destination_parent_directory = os.path.dirname(destination_directory)
-        if not os.path.isdir( destination_parent_directory ):
-            os.makedirs( destination_parent_directory )
-        shutil.move( source_directory, destination_directory )
+        destination_directory = os.path.abspath(os.path.join(destination_dir))
+        if not os.path.isdir(destination_directory):
+            os.makedirs(destination_directory)
+        for dir_entry in os.listdir(source_directory):
+            source_entry = os.path.join(source_directory, dir_entry)
+            if os.path.islink(source_entry):
+                destination_entry = os.path.join(destination_directory, dir_entry)
+                os.symlink(os.readlink(source_entry), destination_entry)
+                os.remove(source_entry)
+            else:
+                shutil.move(source_entry, destination_directory)
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
         # <action type="move_directory_files">