diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 6bb803afbfd..4cd121c7391 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -31,12 +31,9 @@ def main():
 
     testing_shed_tools = testing_migrated_tools or testing_installed_tools
     if testing_shed_tools:
-        # Store a jsonified dictionary of tool_id : GALAXY_TEST_FILE_DIR pairs.
-        galaxy_tool_shed_test_file = 'shed_tools_dict'
         # We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
         tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
     else:
-        galaxy_tool_shed_test_file = None
         framework_test = _check_arg( '-framework' )  # Run through suite of tests testing framework.
         if framework_test:
             tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
@@ -118,7 +115,7 @@ def main():
         if testing_shed_tools:
             driver_util.setup_shed_tools_for_test(
                 app,
-                galaxy_tool_shed_test_file,
+                galaxy_test_tmp_dir,
                 testing_migrated_tools,
                 testing_installed_tools,
             )
@@ -154,13 +151,6 @@ def main():
         )
 
         success = driver_util.nose_config_and_run()
-
-        # TODO: just put this in tempdir being managed for this test.
-        if galaxy_tool_shed_test_file is not None:
-            try:
-                os.unlink( galaxy_tool_shed_test_file )
-            except:
-                log.info( "Unable to remove file: %s" % galaxy_tool_shed_test_file )
     except:
         log.exception( "Failure running tests" )
 
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index 0b6d51a00d1..60c27aa3652 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -337,8 +337,10 @@ def cleanup_directory(tempdir):
         pass
 
 
-def setup_shed_tools_for_test(app, galaxy_tool_shed_test_file, testing_migrated_tools, testing_installed_tools):
+def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_installed_tools):
     """Modify Galaxy app's toolbox for migrated or installed tool tests."""
+    # Store a jsonified dictionary of tool_id : GALAXY_TEST_FILE_DIR pairs.
+    galaxy_tool_shed_test_file = os.path.join(tmpdir, 'shed_tools_dict')
     shed_tools_dict = {}
     if testing_migrated_tools:
         has_test_data, shed_tools_dict = parse_tool_panel_config(MIGRATED_TOOL_PANEL_CONFIG, shed_tools_dict)