Old tRNAscan-SE in containers and environments

[fischuu]

Hi, I am facing a strange issue with the bakta dependency tRNAscan-SE. When I install bakta into a plain mamba environment using this yaml-file (environment.yml),

name: bakta
channels:
  - bioconda
  - conda-forge
dependencies:
  - bakta=1.9.4

running this command

mamba env create -f environment.yml

the installed trnascan version is apparently totally wrong. It seems, it installs version 1.4 from 1997!? Adding the corresponding dependency (= adding - trnascan-se=2.0.11 to the environment) does not help, it still only installs the version 1.4.

Further, when I start one of the precompiled container from biocontainer like this

docker run -it quay.io/biocontainers/bakta:1.9.4--pyhdfd78af_0

I also have only trnascan-1.4 available. I tried randomly older images from biocontainers and they all behave similar. As consequence bakta fails to run, as it is looking for the trnascan-se executable and it fails with the error tRNAscan-SE error! error code: 2

The same happens when I overwrite the oschwengers entrypoint image like this

docker run -it --entrypoint /bin/bash oschwengers/bakta

and make it interactively usable, also there I only find trnascan-1.4, but not the se version.

Any hints what goes wrong here for me are greatly appreciated :)

EDIT: Actually, I found the bin, it is called tRNAscan-se , so apparently my error has some other origin than I assumed, so please ignore this issue. I will update it, once I found the solution