Error on tool execution since upgrading to v19_09

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Hi,

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.

thanks,
-Will

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There is an important section in the 19.09 release notes about tool configuration files: https://docs.galaxyproject.org/en/master/releases/19.09_announce.html#tool-configuration-file-handling-changes

Are your tools from local toolshed perhaps loaded from a separate configuration file? That could be one of the causes I can think of (and you’d need to change Galaxy’s configuration as described in the above linked document)

As of the is not bound to a Session error, we believe we have fixed that, but it took plenty of PRs over time, please make sure you are running the latest commit of the release_19.09 branch.

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Hi Marten,

Thank you for your reply. I had read the 19.09 release notes prior to upgrading, but didn’t think I needed to modify my configuration. However, with some changes on the tool configuration I was able to fix my problem.

thanks again!
-Will

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Hello, this was very helpful as I had the same issue where installed tool panel tools didn’t appear after upgrade from 19.05 to 19.09. Since I am using all the default config files, I didn’t think I would have to change anything in the galaxy.yml, but turns out I did.

In 19.05, I had this line commented out:

#tool_config_file: config/tool_conf.xml,config/shed_tool_conf.xml

and I was still using the default config/tool_conf.xml.sample.

In 19.09, to make the tools display again, I had to uncomment it. I also copied the tool_conf.xml.sample to tool_conf.xml.

I’m pretty new to galaxy so I thought I would check if this is the expected behavior or if I’ve missed something.

Thanks again,
Rebecca

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