diff --git a/hierarchical_object_store_conf.xml.sample b/hierarchical_object_store_conf.xml.sample
new file mode 100644
index 00000000000..38e61944a9f
--- /dev/null
+++ b/hierarchical_object_store_conf.xml.sample
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<backends>
+    <backend name="files1" type="disk" weight="1">
+        <files_dir path="database/files1"/>
+        <extra_dir type="temp" path="database/tmp1"/>
+        <extra_dir type="job_work" path="database/job_working_directory1"/>
+    </backend>
+    <backend name="files2" type="disk" weight="1">
+        <files_dir path="database/files2"/>
+        <extra_dir type="temp" path="database/tmp2"/>
+        <extra_dir type="job_work" path="database/job_working_directory2"/>
+    </backend>
+</backends>
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 66f2ad682f6..1931a4eebb2 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -59,6 +59,7 @@ def main():
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
     tool_data_table_config_path = 'tool_data_table_conf.xml'
     tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
+    use_hierarchical_object_store = os.environ.get( 'GALAXY_USE_HIERARCHICAL_OBJECT_STORE', False )
     if os.path.exists( 'tool_data_table_conf.test.xml' ):
         tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
@@ -153,6 +154,10 @@ def main():
         if tool_dependency_dir is not None:
             kwargs['tool_dependency_dir'] = tool_dependency_dir
 
+        if use_hierarchical_object_store:
+            kwargs['object_store'] = 'hierarchical'
+            kwargs['hierarchical_object_store_config_file'] = 'hierarchical_object_store_conf.xml.sample'
+
         # Build the Universe Application
         app = UniverseApplication( job_queue_workers = 5,
                                    id_secret = 'changethisinproductiontoo',