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StaPH-B
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
I've removed the lines for caching. I think this, in general, saves space in our GA repo, but I believe the cache is stopping Freyja from being created anew each...
### What tool are you looking for and why? Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically...
Lots of versions upgraded Might have to edit a dockerfile in order to trigger the updated workflows....just starting a draft PR for now, and then I can test later when...
Pull Request (PR) checklist: - [x] Include a description of what is in this pull request in this message. - [x] The dockerfile successfully builds to a test target for...
Pull Request (PR) checklist: - [ ] Include a description of what is in this pull request in this message. - [ ] The dockerfile successfully builds to a test...
### What tool are you looking for and why? [kronaTools ](https://github.com/marbl/Krona/tree/master/KronaTools) is a useful set of scripts that I'm currently using to create krona plots from kraken2 outputs. I have...
### What functionality is this repo missing? We have several templates available in [dockerfile-template](https://github.com/StaPH-B/docker-builds/tree/master/dockerfile-template), but there could be more that may be useful. Additional templates: [ ] R-packages (like ggtree)...
Instead of using the older Dockerfiles for medaka, I copied the artic version [1.24-1.11.1 Dockerfile](https://github.com/StaPH-B/docker-builds/blob/master/artic/1.2.4-1.11.1/Dockerfile) and just removed all the artic lines. The prior medaka Dockerfile is for version 1.2.0,...
### What container needs an update? Add citation for the 3 or so docker images that contain RGDv2. example, update readme's with a link to the publication: https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0-RGDv2/README.md https://www.frontiersin.org/articles/10.3389/fmicb.2023.1225207/full I...
### What tool are you looking for and why? Verkko is an hybrid assembler! It's very useful when you have both Hifi and ONT sequencing data. But I'm having issues...
