Hi! I think currently the best solution to run the braker3 tool is to use the Docker/Singularity official image, which includes an official license for genemark.
If you’re using TPV on your instance, you can do something like this: infrastructure-playbook/files/galaxy/tpv/tools.yml at 5ea1efa5390ebb259d300dc2c09f946377b407ac · usegalaxy-eu/infrastructure-playbook · GitHub
The tool was written to work in theory with conda package and manual install/license config, but in practice it’s too complicated to make it work like this.