/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.
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 Instead its about a version of a library that’s used internally by the tool, but in an outdated way that’s not recommended anymore.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.
