diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 67fb063293e..84e58f7e1a5 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -54,6 +54,7 @@ def main():
             use_test_file_dir=not testing_shed_tools,
             default_install_db_merged=True,
             default_tool_conf=default_tool_conf,
+            datatypes_conf=datatypes_conf_override,
         )
 
     app = None
@@ -61,12 +62,8 @@ def main():
 
     if start_server:
         # ---- Build Application --------------------------------------------------
-        kwargs = dict( shed_tool_data_table_config=shed_tool_data_table_config,
-                       update_integrated_tool_panel=False, )
+        kwargs = dict( shed_tool_data_table_config=shed_tool_data_table_config )
         kwargs.update(galaxy_config)
-        if datatypes_conf_override:
-            kwargs[ 'datatypes_config_file' ] = datatypes_conf_override
-
         app = driver_util.build_galaxy_app(kwargs)
         server_wrapper = driver_util.launch_server(
             app,
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index f48b5344b6d..8f26d3cb24d 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -98,6 +98,8 @@ def setup_galaxy_config(
     enable_tool_shed_check=False,
     default_tool_conf=None,
     shed_tool_conf=None,
+    datatypes_conf=None,
+    update_integrated_tool_panel=False,
 ):
     """Setup environment and build config for test Galaxy instance."""
     if not os.path.exists(tmpdir):
@@ -173,13 +175,15 @@ def setup_galaxy_config(
         tool_data_table_config_path=tool_data_table_config_path,
         tool_parse_help=False,
         tool_path=tool_path,
-        update_integrated_tool_panel=False,
+        update_integrated_tool_panel=update_integrated_tool_panel,
         use_tasked_jobs=True,
         use_heartbeat=False,
         user_library_import_dir=user_library_import_dir,
     )
     config.update(database_conf(tmpdir))
     config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
+    if datatypes_conf is not None:
+        config['datatypes_config_file'] = datatypes_conf
     if enable_tool_shed_check:
         config["enable_tool_shed_check"] = enable_tool_shed_check
         config["hours_between_check"] = 0.001
diff --git a/test/tool_shed/functional_tests.py b/test/tool_shed/functional_tests.py
index 97f591c9263..d55ec50176c 100644
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -146,6 +146,7 @@ def main():
                 default_tool_data_table_config_path=default_tool_data_table_config_path,
                 enable_tool_shed_check=True,
                 shed_tool_conf=galaxy_shed_tool_conf_file,
+                update_integrated_tool_panel=True,
             )
         )
         print "Galaxy database connection:", kwargs["database_connection"]