I run a private Galaxy instance and a toolshed. I recently upgraded from 19_05 to 19_09 and also moved to python3. Since this upgrade, my tools from the local toolshed disappeared from the ‘Tools’ pane. All tools from my toolshed were contained with a separate target section within the Tools pane, and that section header has disappeared from the user interface too. Within the Galaxy admin interface the tools are still shown as installed. If I uninstall and the install a tool from my local toolshed (and re-enter the target section), then the tools return to the Tools pane. However, when I try to run these tools I get an error:
Instance <ToolShedRepository at 0x7f4b5c113610> is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: http://sqlalche.me/e/bhk3)
There are some tickets on the galaxy github repo about this error message, but they have all been resolved through commits that I believe I have pulled in or the posted work around does not resolve the issue.
Any help getting past this error would be appreciated.