diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 6950f1b661e..c04fc9d4201 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -117,11 +117,9 @@ def main():
         galaxy_config = driver_util.setup_galaxy_config(
             galaxy_db_path,
             use_test_file_dir=not testing_shed_tools,
+            default_install_db_merged=True,
         )
 
-        database_conf = driver_util.database_conf(galaxy_db_path)
-        install_database_conf = driver_util.install_database_conf(galaxy_db_path, default_merged=True)
-
     # Data Manager testing temp path
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
     data_manager_test_tmp_path = tempfile.mkdtemp( prefix='data_manager_test_tmp', dir=galaxy_test_tmp_dir )
@@ -143,8 +141,6 @@ def main():
                        auto_configure_logging=logging_config_file is None,
                        data_manager_config_file=data_manager_config_file )
         kwargs.update(galaxy_config)
-        kwargs.update(database_conf)
-        kwargs.update(install_database_conf)
         if datatypes_conf_override:
             kwargs[ 'datatypes_config_file' ] = datatypes_conf_override
         # If the user has passed in a path for the .ini file, do not overwrite it.
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index ddcec16fa31..142a91a5689 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -72,7 +72,7 @@ def build_logger():
     return log
 
 
-def setup_galaxy_config(tmpdir, use_test_file_dir=False):
+def setup_galaxy_config(tmpdir, use_test_file_dir=False, default_install_db_merged=True):
     """Setup environment and build config for test Galaxy instance."""
     if not os.path.exists(tmpdir):
         os.makedirs(tmpdir)
@@ -124,6 +124,9 @@ def setup_galaxy_config(tmpdir, use_test_file_dir=False):
         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 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 881fdb58658..d57d13a513d 100644
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -88,8 +88,6 @@ def main():
     os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir
     print "Directory location for hgweb.config:", hgweb_config_dir
     toolshed_database_conf = driver_util.database_conf(shed_db_path, prefix="TOOL_SHED")
-    galaxy_database_conf = driver_util.database_conf(galaxy_db_path)
-    install_database_conf = driver_util.install_database_conf(galaxy_db_path, default_merged=False)
     tool_shed_global_conf = driver_util.get_webapp_global_conf()
     tool_shed_global_conf[ '__file__' ] = 'tool_shed_wsgi.ini.sample'
     kwargs = dict( admin_users='test@bx.psu.edu',
@@ -113,7 +111,6 @@ def main():
                    use_heartbeat=False )
     kwargs.update(toolshed_database_conf)
     print "Tool shed database connection:", toolshed_database_conf["database_connection"]
-    print "Galaxy database connection:", galaxy_database_conf["database_connection"]
 
     # Generate the tool_data_table_conf.xml file.
     file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template )
@@ -174,9 +171,8 @@ def main():
                        tool_config_file=[ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
                        tool_sheds_config_file=galaxy_tool_sheds_conf_file,
                        tool_data_table_config_path=galaxy_tool_data_table_conf_file )
-        kwargs.update(driver_util.setup_galaxy_config(galaxy_db_path, use_test_file_dir=False))
-        kwargs.update(galaxy_database_conf)
-        kwargs.update(install_database_conf)
+        kwargs.update(driver_util.setup_galaxy_config(galaxy_db_path, use_test_file_dir=False, default_install_db_merged=False))
+        print "Galaxy database connection:", kwargs["database_connection"]
         # ---- Build Galaxy Application --------------------------------------------------
         galaxyapp = GalaxyUniverseApplication( **kwargs )