[Repo Request]: Updating images with databases #1397
Description
What functionality is this repo missing?
We update the Freyja image on a weekly basis to incorporate the latest version of its database. Freyja’s database changes so frequently that creating a new image for every individual update would be too burdensome. In contrast, tools like TB-Profiler and AMRFinder have more stable databases with infrequent updates and clearly versioned releases. For those, I believe it is both practical and beneficial to create new images manually as needed to align with their tagged versions.
However, there are tools whose database versions are either not explicitly provided or not controlled by the tool maintainers themselves. In such cases, regular, time-based rebuilds (monthly? quarterly?) may allow for these tools to use more-current databases.
I reviewed the images in this repository, I think these are the images that may have benefit from auto-building and deployment. There are likely more.
- abricate (abricate downloads databases and gives the date they were downloaded. I'm not 100% sure the urls are still good though...)
- emmtyper
- emmtypingtool
- freyja (for other organisms)
- genomad
- meningotype
- mykrobe
- plassembler
- seroba (but I imagine this would be eclipsed by seroba 2)
- staramr
- tiptoft
- vibrant (?)
I'd also like for there to be something for mlst typing. Candidates include srst3 and pymlst.
There are also tools for which we could update the database, like ngmaster, but there needs to be a new dockerfile that includes the appropriate "update database" or "redownload database" command.