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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Can GeneMark be run somewhere else and provided as --other_gff to funannotate in Docker? #967

Closed MichaelFokinNZ closed 8 months ago

MichaelFokinNZ commented 8 months ago

Hi, I struggle somehow to build docker image with genemark and to understand what required for the latest funannotate docker image 1.8.16. A bit different instructions for docker here https://funannotate.readthedocs.io/en/latest/install.html# and there https://funannotate.readthedocs.io/en/latest/docker.html

I assume genemark is needed, what about signalP and repbase?

And the subj - if I run Genemark somewhere else on the same assemble provided to funannotate predict, can the output be used by EVM, say with --other_gff option?