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AlexanderLabWHOI / EUKulele

Automatic eukaryotic taxonomic classification
MIT License
26 stars 7 forks source link

Improve DB download option #65

Open paulzierep opened 2 months ago

paulzierep commented 2 months ago

We're currently working on wrapping this tool for Galaxy (https://usegalaxy.org/). When trying to set up the DB we discovered, that the DB download and generation logic is a bit difficult to use, since often two tax files are downloaded and also since Diamond needs to create an index. Would you mind uploading the DBs (only the 4 dataset that are needed) to zenode, or would you mind if we do that ? That would make it easy to include the DBs in Galaxy and make your great tool accessible via Galaxy ? Best, Paul

akrinos commented 1 week ago

Hi @paulzierep, sincere apologies for the delay in responding to you. I am happy to make the databases accessible via Zenodo, but in that case would you also need that to be the default download behavior in the tool?

paulzierep commented 1 week ago

Hi @akrinos, thanks for the response, for us it would be ideal if we could use the DBs using the --reference_dir flag. It would also be great if the DB stored in zenodo already has the diamond index since that takes by far the longest time to create. Whether you want to use these zenodo links in the tool behavior is up to you (but I don't see any downside and it seems like a more consistent logic then the currently implemented one). Let me know if you need any further clarification.