--- a/README.rst	Thu Jan 16 10:40:43 2025 +0000
+++ b/README.rst	Tue Jul 01 14:01:14 2025 +0000
@@ -1,41 +1,40 @@
 Braker3
 =======
 
-This tool is not in IUC because of the license issues with GeneMark and
-ProtHint that makes it impossible to test it using CI.
+This wrapper runs BRAKER3 using the official Docker image: ``teambraker/braker3``.
 
-GeneMark and ProtHint
----------------------
+It does not require any longer a custom installation of GeneMark on the host system, as these are bundled inside the container.
+
+Docker container
+----------------
 
-Braker requires GeneMark to predict gene, but due to licensing issues, we
-are not allowed to distribute GeneMark automatically.
+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:
 
-Braker also requires ProtHint to use protein sequences as hints to predict
-genes, but, again, due to licensing issues, we are not allowed to distribute
-ProtHint automatically.
+.. code-block:: xml
 
-To use Braker3, the Galaxy administrator needs to install
-GeneMark, and set the ``GENEMARK_PATH`` variable on the job destination.
+    <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).
 
-The only working version of GeneMark to install needs to be downloaded from
-http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz
-This archive also contains ProtHint and various other tools in specific versions needed by Braker3.
+Running
+-------
 
-Unzip it, and set the ``GENEMARK_PATH`` variable to point to the extracted ``bin``
-directory.
+To run this tool during development, use Planemo with Docker support enabled:
 
-Also set the ``PROTHINT_PATH`` variable on the job destination, pointing to the extracted
-``bin/gmes/ProtHint/bin/`` directory
+.. code-block:: bash
 
-Running tests
--------------
+    planemo serve --docker
+    planemo test --docker
 
-Tests require working GeneMark and ProtHint installations, which means
-both GENEMARK_PATH and PROTHINT_PATH are set in job_conf_braker3.xml.
+There is no longer any need to manually set ``GENEMARK_PATH`` or ``PROTHINT_PATH`` via the job configuration.
 
-You should then use the ``--job_config_file job_conf_braker3.xml``
-option for planemo commands.
+Testing
+-------
 
-You should also copy a valid GeneMark license (from
-http://topaz.gatech.edu/GeneMark/license_download.cgi) in
-test-data/gm_key_64.
\ No newline at end of file
+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.