Which conainer repo is used?

[BioinfoTongLI]

Hi there!
thanks for creating this repo. Hopefully I will push some of my modules soon.
I am just wondering are you guys pushing the containers into public repos or are they simply local for now?
Thanks!

Tong

[krokicki]

Hi Tong,
For now we are using a Biocontainers-like repo here:
https://github.com/JaneliaSciComp/containers

We could create something like that in BIoImageTools as well. I think that could help with reusability across workflow systems (Nextflow, Galaxy, etc.) but it's of course also possible to just commit the Dockerfiles here, or use Biocontainers.

[BioinfoTongLI]

Hi Konrad,
thanks for your prompt reply!
sorry, maybe I wasn't clear.
I meant where are the built images stored.
like in this line:
https://github.com/BioImageTools/nextflow-modules/blob/main/modules/bits/cellpose/main.nf#L2
I couldn't find bioimagetools/cellpose:2.2.3-dask2023.10.1-py11 in quay.io nor in dockerhub

[krokicki]

Ah, sorry, I think those modules might be a bit of a mess because we moved them here:
https://github.com/JaneliaSciComp/nextflow-modules/blob/main/modules/janelia/cellpose/main.nf
We'll get that fixed, but I'm not yet sure which modules will go to which repo. Maybe we can use BioImageTools for modules we want to collaborate on?

Anyway, after trying many different container repositories, we've settled on GitHub Container Repository (GHCR). It's working really well for us:
https://github.com/orgs/JaneliaSciComp/packages?repo_name=containers

We can duplicate this kind of structure in BioImageTools if you think it would be useful.