Minimal script to operate on toolbox

get_toolbox.py

from galaxy.app import GalaxyManagerApplication
from galaxy.tool_shed.cache import ToolShedRepositoryCache


global_conf = {
    "shed_tool_config_file": "shed_tool_conf.xml",
}
app = GalaxyManagerApplication(**global_conf)
app.tool_shed_repository_cache = app._register_singleton(ToolShedRepositoryCache)
app._configure_tool_data_tables(from_shed_config=False)
app._configure_toolbox()
toolbox = app.toolbox

toolbox.patch

diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 4257795d29..1c8d6c1f46 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -194,8 +194,8 @@ class AbstractToolBox(ManagesIntegratedToolPanelMixin):
         # (e.g., shed_tool_conf.xml) files include the tool_path attribute within the <toolbox> tag.
         self._tool_root_dir = tool_root_dir
         self.app = app
-        self._tool_watcher = self.app.watchers.tool_watcher
-        self._tool_config_watcher = self.app.watchers.tool_config_watcher
+        self._tool_watcher = None
+        self._tool_config_watcher = None
         self._filter_factory = FilterFactory(self)
         self._tool_tag_manager = self.tool_tag_manager()
         self._init_tools_from_configs(config_filenames)