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"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
author genouest
date Tue, 05 Oct 2021 12:35:42 +0000
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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1 # Braker
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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3 This tool is not in IUC because of the license issues with GeneMark and ProtHint that makes it impossible to test it using CI.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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5 ## GeneMark
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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7 Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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9 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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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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11 ## ProtHint
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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13 Braker can use ProtHint to use protein sequences as hints to predict genes, but due to licensing issues, we are not allowed to distribute ProtHint automatically.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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15 If you want to use it, the Galaxy administrator needs to install ProtHint, and set the `PROTHINT_PATH` variable on the job destination.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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17 ## Running tests
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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19 Tests require working GeneMark and ProtHint installations, which means both GENEMARK_PATH and PROTHINT_PATH are set.
e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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e50ea151f221 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"
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21 You should also copy a valid GeneMark license (from http://topaz.gatech.edu/GeneMark/license_download.cgi) in test-data/genemark_license.gm_key