diff --git a/gga_load_data.py b/gga_load_data.py
index 8a1408c9fdb8046f20d6332103fbde56ac22f28f..058463285738421c0a389016e699c7fb074859c2 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+import re
 
 import bioblend
 import argparse
@@ -183,7 +184,8 @@ class LoadData(speciesData.SpeciesData):
                             logging.info("Skipping useless file '%s'" % single_file)
                             continue
 
-                        single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file)
+                        single_file_relative_path = re.sub(data_dir_root, CONTAINER_DATA_DIR_ROOT, single_file)
+                        single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file_relative_path)
 
                         logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file_path_in_container, ftype, clean_name))
                         datasets = prj_lib.upload_from_galaxy_fs(