diff -r 29ce93a13ac7 tools/data_source/upload.py
--- a/tools/data_source/upload.py	Mon Feb 10 13:22:47 2014 -0500
+++ b/tools/data_source/upload.py	Tue May 27 10:54:42 2014 -0400
@@ -4,7 +4,7 @@
 # WARNING: Changes in this tool (particularly as related to parsing) may need
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
 
-import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii
+import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii, subprocess
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model
@@ -352,6 +352,19 @@
                      stdout = 'uploaded %s file' % dataset.file_type )
         json_file.write( to_json_string( info ) + "\n" )
 
+def _chown( dataset ):
+    if ( dataset.type != 'file' ):
+        return
+
+    try:
+        cmd = [ '/usr/bin/sudo', '-E', '/home/galaxy/server-conf/chown_script.pl', dataset.path ]
+        sys.stdout.write( 'Changing ownership of %s with: %s' % ( dataset.path, ' '.join( cmd ) ) )
+        p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE )
+        sys.stdout.write( p.stdout.read() )
+        sys.stderr.write( p.stderr.read() )
+    except Exception, e:
+        sys.stderr.write( 'Changing ownership of uploaded file %s failed: %s' % ( dataset.path, str( e ) ) )
+
 def __main__():
 
     if len( sys.argv ) < 4:
@@ -372,6 +385,9 @@
         except:
             print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id
             sys.exit( 1 )
+
+        _chown( dataset )   
+
         if dataset.type == 'composite':
             files_path = output_paths[int( dataset.dataset_id )][1]
             add_composite_file( dataset, registry, json_file, output_path, files_path )