diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index 7d80a8a7806..953a829208f 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -85,6 +85,7 @@ def setup_galaxy_config(
     use_test_file_dir=False,
     default_install_db_merged=True,
     default_tool_data_table_config_path=None,
+    enable_tool_shed_check=False,
 ):
     """Setup environment and build config for test Galaxy instance."""
     if not os.path.exists(tmpdir):
@@ -143,7 +144,9 @@ def setup_galaxy_config(
     )
     config.update(database_conf(tmpdir))
     config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
-
+    if enable_tool_shed_check:
+        config["enable_tool_shed_check"] = enable_tool_shed_check
+        config["hours_between_check"] = 0.001
     if tool_dependency_dir:
         config["tool_dependency_dir"] = tool_dependency_dir
         # Used by shed's twill dependency stuff - todo read from
diff --git a/test/tool_shed/functional_tests.py b/test/tool_shed/functional_tests.py
index c2cf566fdcb..ce04f3ea45a 100644
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -132,9 +132,7 @@ def main():
         # Generate shed_data_manager_conf.xml
         if not os.environ.get( 'GALAXY_SHED_DATA_MANAGER_CONF' ):
             open( galaxy_shed_data_manager_conf_file, 'wb' ).write( shed_data_manager_conf_xml_template )
-        kwargs = dict( enable_tool_shed_check=True,
-                       hours_between_check=0.001,
-                       migrated_tools_config=galaxy_migrated_tool_conf_file,
+        kwargs = dict( migrated_tools_config=galaxy_migrated_tool_conf_file,
                        shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
                        shed_tool_data_table_config=shed_tool_data_table_conf_file,
                        shed_tool_path=galaxy_shed_tool_path,
@@ -146,7 +144,8 @@ def main():
                 galaxy_db_path,
                 use_test_file_dir=False,
                 default_install_db_merged=False,
-                default_tool_data_table_config_path=default_tool_data_table_config_path
+                default_tool_data_table_config_path=default_tool_data_table_config_path,
+                enable_tool_shed_check=True,
             )
         )
         print "Galaxy database connection:", kwargs["database_connection"]