BRAKER3 fails on Galaxy Europe with 'Genemark not installed' error

[jing666]

:
When running BRAKER3 for genome annotation on Galaxy Europe, the job fails with:
Error: "Genemark is not installed properly on this Galaxy server."

1. Upload genome (FASTA) and protein-seq data.
2. Run BRAKER3 with default parameters.
3. Job crashes during execution.

Expected vs. Actual Behavior:

• Expected: Successful annotation.
• Actual: Tool dependency error (Genemark missing).

Troubleshooting Attempted:

• Checked Galaxy Europe documentation.
• Re-ran with different input data → same error.

Question:
Is Genemark intentionally unavailable on Galaxy Europe? Are there workarounds (e.g., alternative tools)?

[jennaj]

Welcome, @jing666

Correct, the Genmark annotation is proprietary and cannot be hosted at the public Galaxy servers.

The tool wrappers are designed to support the extra annotation when run in a private environment. This is true with the Braker3 tool and others that can incorporate the annotation.

@igor

Have you changed GenMark settings during the job setup?
The description says:
GeneMark is not a free software, to use it download and unzip a license from GeneMark™ download (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators, it might not be available on this server.
You need a license for this option.

If you are interested in doing this, the Docker version of Galaxy would be the easiest to deploy and run for personal use.

@jennaj

Docker Galaxy

Much comes pre-configured, and common administrative tasks are simpler to implement and maintain. Be sure to review the repository’s README for these custom instructions.

Docker Galaxy

• Galaxy Docker - Galaxy Community Hub
• bgruening/docker-galaxy-stable chat at https://matrix.to/#/#bgruening_docker-galaxy-stable:gitter.im

Then more details about this exact tool can be found in the development repository (tool form → See in Toolshed) → https://toolshed.g2.bx.psu.edu/repository?repository_id=36c87739f9e2cecf

GeneMark

Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically.

If you want to use it, the Galaxy administrator needs to install GeneMark, and set the GENEMARK_PATH variable on the job destination.

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Hope this helps to explain the situation, and maybe gives you some options for using it!