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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
author genouest
date Wed, 06 Sep 2023 09:50:12 +0000
parents cf241e076f7b
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
genouest
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1 Braker
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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2 =======
cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
genouest
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4 This tool is not in IUC because of the license issues with GeneMark and ProtHint that makes it impossible to test it using CI.
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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6 GeneMark
ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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9 Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically.
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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11 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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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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13 ProtHint
ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
genouest
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15 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.
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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17 If you want to use it, the Galaxy administrator needs to install ProtHint, and set the `PROTHINT_PATH` variable on the job destination.
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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19 Running tests
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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22 Tests require working GeneMark and ProtHint installations, which means both GENEMARK_PATH and PROTHINT_PATH are set.
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cf241e076f7b planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
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ac13de106677 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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24 You should also copy a valid GeneMark license (from http://topaz.gatech.edu/GeneMark/license_download.cgi) in test-data/genemark_license.gm_key