TSEBRA-input files

[jennaj]

@rachelihadjez

TSEBRA

Hi @rachelihadjez

There are some licensing issue with these tools, which is probably part of the confusion.

BRAKER3 runs TSEBRA internally. The result in Galaxy is the single primary output: braker.gtf. That is the first top output listed here →

• GitHub - Gaius-Augustus/BRAKER: BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Then this is in the Galaxy repository, and may explain why some of the other files are not output? If you search the tool panel with the keywork “braker” you’ll find the tools and versions of those tool that can be hosted on a public server. If you can’t find one of the tools mentioned in a publication or in Github, the licensing issue is probably why but you can ask.

• galaxy-tools/tools/braker at master · genouest/galaxy-tools · GitHub

Then, to complicated it TSEBRA can also be run by itself, and that can use another file that is created by one of the tools that Galaxy cannot host on public sites, but you could upload it (the “hints” files).

• GitHub - Gaius-Augustus/TSEBRA: TSEBRA: Transcript Selector for BRAKER
• tools-iuc/tools/tsebra at main · galaxyproject/tools-iuc · GitHub

Does this help?