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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
MIT License
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Change the defalt gene prediction method to Prodigal for genoem and metagenome #666

Closed igormakunin closed 2 years ago

igormakunin commented 2 years ago

https://github.com/galaxyproteomics/tools-galaxyp/blob/0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml#L20

Can you please change the default gene prediction method (--genepred) to Prodigal for genome and metagenome data? The eggNOG site use Prodigal as default, and Blastx-like option has the following warning: not recommended for Bacteria genome-sized contigs. Many Galaxy users submit jobs with default settings, and use Blastx-like method with long contigs, resulting in very long run time.

bgruening commented 2 years ago

@igormakunin thanks for the report. This one might fix it: https://github.com/galaxyproteomics/tools-galaxyp/pull/667