Which conainer repo is used? #1

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1. krokicki commented on Mar 27, 2024

   

   krokicki

   on Mar 27, 2024

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   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.
2. BioinfoTongLI commented on Mar 27, 2024

   

   BioinfoTongLI

   on Mar 27, 2024

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   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
3. krokicki commented on Mar 27, 2024

   

   krokicki

   on Mar 27, 2024

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   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.