Use GMS-Artic images through dockerhub

genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

GNU Affero General Public License v3.0

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Use GMS-Artic images through dockerhub #4

Closed sylvinite closed 2 years ago

sylvinite commented 3 years ago

What needs to be done: Images built under https://github.com/genomic-medicine-sweden/gms-artic/blob/master/scripts/build_singularity_containers.sh should have a fallback to pull them from dockerhub

[x] Set up Dockerhub account
[x] Set up solution to push images to Dockerhub (github actions)
[x] Set up solution to pull images from dockerhub
[x] Automatically update the container on the local work directory

Suggestions on how to get it done: Dockerhub, remote build

What are the arguments for getting it done: The reason for running singularity is usually the exact same reason as to why its not possible to build images with the same account

talnor commented 3 years ago

Do we have a dockerhub account set up?

talnor commented 3 years ago

nextflow automatically pulls images from Dockerhub if we set process.container = "dockerhub-user/image-name" for singularity.

JD2112 commented 3 years ago

singularity { singularity.enabled = true singularity.autoMounts = true if ( params.medaka || params.nanopolish ){ // process.container = "file:///${baseDir}/artic-ncov2019-nanopore.sif" // process.container = "docker://quay.io/jd2112/gms-artic:nanopore" process.container = "library://jd2112/gms-artic-illumina/gms-artic-nanopore.sif:latest" } else if (params.illumina) { // process.container = "file:///${baseDir}/artic-ncov2019-illumina.sif" // process.container = "docker://quay.io/jd2112/gms-artic:illumina" process.container = "library://jd2112/gms-artic-illumina/gms-artic-illumina.sif:latest" }

I add both docker hub container and singularity library container to the config file.