diff README.rst @ 0:3c0865d1172f draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb

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+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.
+
+GeneMark and ProtHint
+---------------------
+
+Braker requires GeneMark to predict gene, but due to licensing issues, we
+are not allowed to distribute GeneMark automatically.
+
+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.
+
+To use Braker3, the Galaxy administrator needs to install
+GeneMark, and set the ``GENEMARK_PATH`` variable on the job destination.
+
+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.
+
+Unzip it, and set the ``GENEMARK_PATH`` variable to point to the extracted ``bin``
+directory.
+
+Also set the ``PROTHINT_PATH`` variable on the job destination, pointing to the extracted
+``bin/gmes/ProtHint/bin/`` directory
+
+Running tests
+-------------
+
+Tests require working GeneMark and ProtHint installations, which means
+both GENEMARK_PATH and PROTHINT_PATH are set in job_conf_braker3.xml.
+
+You should then use the ``--job_config_file job_conf_braker3.xml``
+option for planemo commands.
+
+You should also copy a valid GeneMark license (from
+http://topaz.gatech.edu/GeneMark/license_download.cgi) in
+test-data/gm_key_64.
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