staramr deprecation?

Hello,
I am trying to use the AMR annotation tool Staramr on a fasta-formatted contigs file for the ‘Identification of AMR genes’ tutorial (Hands-on: Identification of AMR genes in an assembled bacterial genome / Identification of AMR genes in an assembled bacterial genome / Genome Annotation). This tutorial shows the most recent update just a few weeks ago (10 June 2025). When I run Staramr I get the following error for all outputs:

/usr/local/lib/python3.9/site-packages/Bio/Application/init.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

Can you advise on whether Staramr is fully deprecated and now unusable, or is there a work-around that I am missing.

Thank you very much.

Hi @park6728,
the depcrecation notice is not about StarAMR, which will continue to be useful. Instead its about a version of a library that’s used internally by the tool, but in an outdated way that’s not recommended anymore.

From my own testing, it appears, however, that you did not paste the full error message but truncated it before the interesting part.
The warning you pasted is just that - a warning, but the real error is with one of the databases used by the tool.

This error is specific to version 0.11.0+galaxy2 of the tool. If you’re using 0.11.0+galaxy0 or 0.10.0+galaxy1 (the exact version recommended in the tutorial) things will just work.

I hope this helps while we’re investigating the db issue with the latest version.

Hi Wolfgang,
thanks very much for the quick reply. I have been successful in using the recommended Galaxy versions for other tutorials and for other parts of this tutorial. However, I don’t see the option to choose a different version of Staramr in my current Galaxy options. Here is what the Staramr implementation looks like for me:

Yeah, just search for staramr again in the tool panel. You’ll find that there are two records for it, one with just the latest version, the other one with all the older ones, for reasons I don’t know atm.
Sorry, should have realized that before.

All good, thanks again!

Matt