I noticed usegalaxy’s version of RGI (5.2.1) is incompatible with the latest CARD database, can someone look into this?
Welcome @luc
I replied to your bug report but let’s post this information publicly too so others can find it!
There was a known problem with the version of the index we provided for the first version of the Galaxy wrapper. These specific errors – one or both lines – happen for anyone who was using it that had a query that “hit” that part of the index model.
WARNING 2025-01-10 17:29:54,919 : Exception: <class ‘ValueError’> → invalid literal for int() with base 10: ‘1Va’ → model_type: variant
WARNING 2025-01-10 17:30:04,032 : partial gene in card reference: OXA-140
Both should likely be respected as warnings and not fail the underlying tool. I see you had jobs that did both! The server index reported the first (and failed) and newer index you loaded up was reporting the second (but was successful, so the warning-only status was adjusted).
The whole Galaxy wrapper is pending an update. If you or anyone reading would like to make more suggestions to improve the wrapper itself further, you may open an issue ticket here. There is already one catch-all Issue but more ideas are welcome! The index will be updated when this happens.
The default tool test works, but this is a very simple input and uses all default settings. The test case is likely not hitting the problematic model. So, this isn’t about the wrapper-index combination and more about that version of the index with any version of RGI that uses it, in or out of Galaxy.
This pending update is one of the reasons why this request to install the tool at server’s other than UseGalaxy.org are still pending.
Thanks for reporting the issue and hope this helps to clarify about what is going on! 
While we are waiting for an update, perhaps Galaxy can provide older CARD databases locally for users to perform exploratory analysis? I loaded databases from the beginning of 2021 and there were no issues.
-lucas
Hi @luc We have @wm75 out right now but he’ll see the ping here when he is back. Maybe something can be done with a warning tag added eg not for production at the UseGalaxy.eu server. Let’s see! 