dessimozlab/oma_standalone repository overview

⁠OMA standalone

OMA standalone is a standalone package that can infer orthologs using the OMA algorithm on custom genomes. It is also possible to export genomes and their homology relations directly from the OMA web-browser and combine them with custom genomes or proteomes.

See https://omabrowser.org/standalone⁠ for more general details.

To infer orthologs with OMA standalone docker / singularity container, you need to bind mount the root directory of your analysis (the directory containing the DB/ folder with the fasta files of the proteomes) into /oma. That root directroy should also contain the parameter file. You can create one with the oma -p command.

⁠Example session:

# create parameter file with default values
docker run --rm -v $(pwd):/oma dessimozlab/oma_standalone:latest oma -p

# start analysis
docker run --rm -v $(pwd):/oma dessimozlab/oma_standalone:latest oma