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Repository braker3
Name: braker3
Owner: genouest
Synopsis: BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .
Type: unrestricted
Revision: 9:bec8f57c9d8e
This revision can be installed: True
Times cloned / installed: 465

Repository README files - may contain important installation or license information

Braker3

This wrapper runs BRAKER3 using the official Docker image: teambraker/braker3.

It does not require any longer a custom installation of GeneMark on the host system, as these are bundled inside the container.

Docker container

BRAKER3 depends on GeneMark for gene prediction from RNA-Seq and protein evidence. Due to licensing issues, these tools could not be redistributed directly, but the official BRAKER3 Docker image includes the required versions.

The wrapper uses this image via the Galaxy <container type="docker"> mechanism:

<container type="docker">teambraker/braker3:v3.0.7.6</container>

2025.07.01: The licensing issue seems to be gone (https://github.com/Gaius-Augustus/BRAKER/issues/629), but using Conda packages is broken at the moment, and not supported by the authors of Braker (https://github.com/Gaius-Augustus/BRAKER/commit/ece9e0f28ea2634b5abbfd0b7cf0a6be5f1bf8db).

Running

To run this tool during development, use Planemo with Docker support enabled:

planemo serve --docker
planemo test --docker

There is no longer any need to manually set GENEMARK_PATH or PROTHINT_PATH via the job configuration.

Testing

Tests no longer rely on custom environment variables. Docker ensures a reproducible and portable environment for development and execution.

job_conf_braker3.xml is now obsolete for this wrapper version.

Contents of this repository

Name Description Version Minimum Galaxy Version
genome annotation 3.0.8+galaxy1 22.05

Categories
Genome annotation - Tools for annotating genomic information