Issue with Python based tools if conda base environment is activated by default

Hi,

I had an issue to test/serve tools which needs Python libraries (e.g. Scanpy, Anndata, Table compute on IUC):

https://gist.github.com/bebatut/f31bdb9342c5032e2c49a0580ec3eaa8

The tools were failing because the needed Python libraries were not found. But if we go inside the conda environment created by Galaxy (mulled-…) and start python, the libraries are there.
Nothing interesting was in the log mentioning that the conda environment was not loaded.

After different tests (different versions of Planemo, conda, Galaxy), I found out that if I remove conda from the path and I do not have the conda base environment activated by default, I can test/serve the tools.

Any idea why?
Thanks

Bérénice

Start by reproducing the failure described in the linked gist through Planemo's test and serve entry points, comparing behavior with and without conda on PATH and the base environment activated. Trace how the Galaxy-created mulled environment is selected and report or correct the environment handling so libraries such as Scanpy and Anndata are found consistently.

Written by the indexing model from the issue text.