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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
children
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2:cf241e076f7b 3:ac13de106677
1 Braker3 1 Braker
2 ======= 2 =======
3 3
4 This tool is not in IUC because of the license issues with GeneMark and 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.
5 ProtHint that makes it impossible to test it using CI.
6 5
7 GeneMark and ProtHint 6 GeneMark
8 --------------------- 7 ---------
9 8
10 Braker requires GeneMark to predict gene, but due to licensing issues, we 9 Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically.
11 are not allowed to distribute GeneMark automatically.
12 10
13 Braker also requires ProtHint to use protein sequences as hints to predict 11 If you want to use it, the Galaxy administrator needs to install GeneMark, and set the `GENEMARK_PATH` variable on the job destination.
14 genes, but, again, due to licensing issues, we are not allowed to distribute
15 ProtHint automatically.
16 12
17 To use Braker3, the Galaxy administrator needs to install 13 ProtHint
18 GeneMark, and set the ``GENEMARK_PATH`` variable on the job destination. 14 ---------
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.
19 16
20 The only working version of GeneMark to install needs to be downloaded from 17 If you want to use it, the Galaxy administrator needs to install ProtHint, and set the `PROTHINT_PATH` variable on the job destination.
21 http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz
22 This archive also contains ProtHint and various other tools in specific versions needed by Braker3.
23
24 Unzip it, and set the ``GENEMARK_PATH`` variable to point to the extracted ``bin``
25 directory.
26
27 Also set the ``PROTHINT_PATH`` variable on the job destination, pointing to the extracted
28 ``bin/gmes/ProtHint/bin/`` directory
29 18
30 Running tests 19 Running tests
31 ------------- 20 --------------
32 21
33 Tests require working GeneMark and ProtHint installations, which means 22 Tests require working GeneMark and ProtHint installations, which means both GENEMARK_PATH and PROTHINT_PATH are set.
34 both GENEMARK_PATH and PROTHINT_PATH are set in job_conf_braker3.xml.
35 23
36 You should then use the ``--job_config_file job_conf_braker3.xml`` 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
37 option for planemo commands.
38
39 You should also copy a valid GeneMark license (from
40 http://topaz.gatech.edu/GeneMark/license_download.cgi) in
41 test-data/gm_key_64.