diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index c99d3666a9d..75ede455dac 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -75,8 +75,9 @@ def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_rev
     # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict.
     shed_tool_conf_dict[ 'config_elems' ] = config_elems
     app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict
-    # Write the current in-memory version of the integrated_tool_panel.xml file to disk.
-    app.toolbox.write_integrated_tool_panel_config_file()
+    if app.config.update_integrated_tool_panel:
+        # Write the current in-memory version of the integrated_tool_panel.xml file to disk.
+        app.toolbox.write_integrated_tool_panel_config_file()
     app.toolbox_search = ToolBoxSearch( app.toolbox )
 def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=False, override=True ):
     """
@@ -1055,7 +1056,7 @@ def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ):
     shed_tool_conf_dict[ 'config_elems' ] = config_elems
     trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict
     trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
-    if uninstall:
+    if uninstall and trans.app.config.update_integrated_tool_panel:
         # Write the current in-memory version of the integrated_tool_panel.xml file to disk.
         trans.app.toolbox.write_integrated_tool_panel_config_file()
 def remove_tool_dependency( trans, tool_dependency ):
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 0c031050cbd..e63d0843eb5 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1088,14 +1088,16 @@ class AdminToolshed( AdminGalaxy ):
         if ( not includes_tools and not includes_repository_dependencies ) or \
             ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ):
             install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
-            if includes_tool_dependencies:
-                install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
+            if includes_tools:
                 shed_tool_conf = kwd[ 'shed_tool_conf' ]
             else:
-                install_tool_dependencies = False
                 # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config
                 # setting points.
                 shed_tool_conf = trans.app.config.migrated_tools_config
+            if includes_tool_dependencies:
+                install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
+            else:
+                install_tool_dependencies = False
             tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
             created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \
                 shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False )