StaPH-B / docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

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[Container Request]: mummer #310

Closed kapsakcj closed 2 years ago

kapsakcj commented 2 years ago

Contact Details

curtis.kapsak@theiagen.com

What tool are you looking for and why?

mummer for calculating ANI values

Looks like mummer v4.x.x is a separate code repo from mummer 3.x.x and older. Probably best to go with latest version, I think? https://github.com/mummer4/mummer

It's on bioconda and biocontainers exist for mummer4 on quay.io, but would be nice to have a StaPH-B docker image available too.

kapsakcj commented 2 years ago

include fastas from Reference Gene Database (v2? v3?) from EDLB

kapsakcj commented 2 years ago

327 PR should close this Issue, but I'd like to keep it open for now. I'll create a second dockerfile that includes the RGDv3 fasta files to be used for ANI. I think this will be very useful for those in the community that are working with enteric pathogens

kapsakcj commented 2 years ago

started dev branch cjk-mummer-RGD for this. Needs testing & polishing before starting a PR

Additionally started PR #399 to add RGDv2 to the fastANI docker image for similar functionality

kapsakcj commented 2 years ago

closed via #405