Error with Scanpy Read10x tool version 1.8.1+galaxy93

[nomadscientist]

That's the error message when I'm running this step with 1.8.1+galaxy93

If it's not a quick fix, we might want to hide the latest version

Originally posted by @wee-snufkin in galaxyproject/training-material#4411 (comment)

[nomadscientist]

[nomadscientist]

@pcm32 @bgruening @wee-snufkin

[bgruening]

This is fixed on EU, isn't it?

[nomadscientist]

Nope just tested it, still fails

[bgruening]

Can you please send me a new error report? This error above is hopefully solved.

[nomadscientist]

Traceback (most recent call last): File "/usr/local/tools/_conda/envs/[email protected]/bin/scanpy-read-10x", line 6, in <module> from scanpy_scripts.cmds import READ_CMD File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy_scripts/__init__.py", line 15, in <module> from . import lib File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy_scripts/lib/__init__.py", line 5, in <module> from ._read import read_10x File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy_scripts/lib/_read.py", line 6, in <module> import scanpy as sc File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy/__init__.py", line 16, in <module> from . import plotting as pl File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy/plotting/__init__.py", line 1, in <module> from ._anndata import ( File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy/plotting/_anndata.py", line 28, in <module> from . import _utils File "/usr/local/tools/_conda/envs/[email protected]/lib/python3.9/site-packages/scanpy/plotting/_utils.py", line 35, in <module> class _AxesSubplot(Axes, axes.SubplotBase, ABC): TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

[nomadscientist]

https://usegalaxy.eu/u/wendi.bacon/h/unnamed-history-7

[bgruening]

Can you please try again? :)

[pcm32]

I tried this on our instance which uses singularity and it is working well. Can the tool be switched to use the singularity container on .eu?

[nomadscientist]

I suspect there are issues with this entire suite, as I've just tried Scanpy RunFDG and it failed, and this is the same for the latest Manipulate AnnData version
(Galaxy Version 0.10.3+galaxy0)
Can you send us some of the workflows you have functioning on your instance Pablo so we can test them (and thereby eliminate user error)?
Currently, these tools break all our tutorials if a user accidentally uses them, so it's a concern