Local workflow with medaka fails with error

Hi all,

I have a problem with running a Workflow on a local instance of Galaxy (running on a Ubuntu server).
In this workflow, a Flye assembly is fed to a Medaka consensus pipeline together with a bunch of fastq files from a MinION run. This workflow runs beautifully on usegalaxy.eu but on my own server I get the follow error:

{ "code_desc": "", "desc": "Fatal error: Exit code 126 ()", "error_level": 3, "exit_code": 126, "type": "exit_code" }

and this is shown in the history:

Because the same workflow runs fine on usegalaxy.eu I guess it has something to do with the installation of medaka because that was not easy. Installing medaka (including the dependencies) from the admin menu always results in an error with Galaxy hanging and need a restart. This seems to be a know issue (see github). So I installed medaka throught the CLI with conda:

conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __medaka@1.7.2 medaka=1.7.2

and then copied everything to the galaxy environment:

cp -r ./mambaforge/envs/__medaka@1.7.2 ./galaxy/dependencies/_conda/envs/

Galaxy now sees medaka tool with it’s dependencies resolved but running the workflow thus gives an error.

Any ideas?
Thanks in advance!

see also: Medaka consensus pipeline error · Issue #5233 · galaxyproject/tools-iuc · GitHub