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comparison README.rst @ 2:cf241e076f7b draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit be0db9109388c0660c9f901f6b7129c0e3e5105c
author genouest
date Tue, 05 Sep 2023 09:40:27 +0000
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1:ca7c12566894 2:cf241e076f7b
1 Braker3
2 =======
3
4 This tool is not in IUC because of the license issues with GeneMark and
5 ProtHint that makes it impossible to test it using CI.
6
7 GeneMark and ProtHint
8 ---------------------
9
10 Braker requires GeneMark to predict gene, but due to licensing issues, we
11 are not allowed to distribute GeneMark automatically.
12
13 Braker also requires ProtHint to use protein sequences as hints to predict
14 genes, but, again, due to licensing issues, we are not allowed to distribute
15 ProtHint automatically.
16
17 To use Braker3, the Galaxy administrator needs to install
18 GeneMark, and set the ``GENEMARK_PATH`` variable on the job destination.
19
20 The only working version of GeneMark to install needs to be downloaded from
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
30 Running tests
31 -------------
32
33 Tests require working GeneMark and ProtHint installations, which means
34 both GENEMARK_PATH and PROTHINT_PATH are set in job_conf_braker3.xml.
35
36 You should then use the ``--job_config_file job_conf_braker3.xml``
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.