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StaPH-B
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Started a dockerfile on a separate branch, medaka-dev. https://github.com/StaPH-B/docker-builds/commit/641a2aeb089f86d063974d73f599b10530a87102 Docker image builds ok locally. Haven't run any data through to verify functionality. Not ready to merge & build on dockerhub...
Need testing and potentially fixing before merging into master & building on dockerhub. These 3 images built successfully, but need to run data through. I'm testing the 1.4.3 version and...
`LABEL container.version` is super vague. It should be `LABEL dockerfile.version`. Intended for tracking multiple versions of a dockerfile for a single program (and it's single version). For example if I...
This: ```Dockerfile # set PATH and perl local settings ENV PATH="${PATH}:/mlst-2.19.0/bin:\ /ncbi-blast-2.9.0+/bin" \ LC_ALL=C ``` uses one layer to set env variables, where as the below examples adds an unnecessary...
Adds dockerfile and README.md for `pbptyper` 1.0.4. The changes include addition of `fastANI` as a screening step & the new flag `pbptyper --check` to check tblastn and fastANI dependencies. The...
### What tool are you looking for and why? because Torsten endorsed Bakta over Prokka. Will not be able to include the Bakta database due to its large size, but...
There's a recent update to flye. According to the notes at https://github.com/fenderglass/Flye/releases/tag/2.9.1, this is a minor release that focuses on fixing bugs. I took the old dockerfile and changed the...
### What container needs an update? There's a new version of MultiQC. https://github.com/ewels/MultiQC/releases/tag/v1.13 I don't mind the biocontainers one, so I'll be using that in the meantime. The [ewels/multiqc](https://hub.docker.com/r/ewels/multiqc/tags) wasn't...
Attempting to resolve issue #444 with blast binary incompatibilities with prokka. @SESchmedes I've pushed this docker image to dockerhub, if you'd like to test out on your cluster. Hoping this...
### What container needs an update? There is a bug in prokka that causes random failures at the blastp step. Potentially need to update container to use pre-built blast binaries...
