Local Galaxy instance.
I upgraded my local galaxy instance to 19.09 from 19.04. No initial issues were observed. No errors.
When I restart Galaxy, all installed “shed_tools” disappear from my gui tools menu. Interesting …
If I delete the intergrated_tool_panel.xml file, the shed_tools reappear in the gui menu when I restart.
Restarting again, and the tools disappear.
It would appear that while the shed_tools are added to the GUI menu correctly, they do not appear to be added to the integrated_tool_panel.xml file ( The contents of tools_config.xml is added to the file, but the shed_tools are never added to this file). If you restart, galaxy reads from the integrated_tools_panel.xml file and therefore no shed_tools. Delete the file and it works until restart.
Any ideas, this one is beyond me…