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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 43caacb959b2d7b842e71737bd645be7ad155a04
author genouest
date Thu, 17 Jul 2025 10:35:48 +0000
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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1 Braker3
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2 =======
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4 This wrapper runs BRAKER3 using the official Docker image: ``teambraker/braker3``.
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6 It does not require any longer a custom installation of GeneMark on the host system, as these are bundled inside the container.
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8 Docker container
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9 ----------------
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11 BRAKER3 depends on GeneMark for gene prediction from RNA-Seq and protein evidence.
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12 Due to licensing issues, these tools could not be redistributed directly, but the official BRAKER3 Docker image includes the required versions.
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14 The wrapper uses this image via the Galaxy `<container type="docker">` mechanism:
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16 .. code-block:: xml
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18 <container type="docker">teambraker/braker3:v3.0.7.6</container>
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20 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,
bec8f57c9d8e planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 1df3cddb1fd83dc0059b5a9cd57dafa9ae4b4f24
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21 and not supported by the authors of Braker (https://github.com/Gaius-Augustus/BRAKER/commit/ece9e0f28ea2634b5abbfd0b7cf0a6be5f1bf8db).
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23 Running
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24 -------
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26 To run this tool during development, use Planemo with Docker support enabled:
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28 .. code-block:: bash
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30 planemo serve --docker
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31 planemo test --docker
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33 There is no longer any need to manually set ``GENEMARK_PATH`` or ``PROTHINT_PATH`` via the job configuration.
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35 Testing
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36 -------
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38 Tests no longer rely on custom environment variables. Docker ensures a reproducible and portable environment for development and execution.
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40 ``job_conf_braker3.xml`` is now obsolete for this wrapper version.