Regenie Docker image

[akotlar]

Hey all, would it be possible add building and pushing a version-tagged regenie docker image. We (Hail team), are building a regenie module, and would like to rely on an official image. Happy to PR a Makefile change if that would help (just need the repo to push to).

Also, would you accept a PR that modified the Dockerfile to exclude ENTRYPOINT? This would make our lives slightly easier, and would make regenie invocation via docker container a bit more uniform with that in a normal shell environment (could copy paste the regenie examples, and when running from docker would make it possible to use environment variables within the regenie command)

[joellembatchou]

Hi,

Docker images are available in here. Thank you for suggesting the removal of ENTRYPOINT (indeed this was not necessary); the Dockerfile has been changed appropriately.

The Makefile has also been edited so that running make docker-build will build the docker image and make docker-test will run a test script (using the exemplar commands from the Regenie webpage) to check the image build.

Cheers,
Joelle

[akotlar]

Awesome thanks Joelle!

[akotlar]

Sorry, to be clear about the image: you aren't actually publishing it to Docker Hub. Would it be possible to do so? This has some implications on integrating the project into an existing build system, and the licensing issues that may entail, even with a compatible license (namely we need to get approval from our legal department to add the entire regenie codebase to our github repo, which is needed to build the image, but referencing a built docker image , published to Docker Hub or some other repository like gcr.io, carries no such complexities). It would be helpful, but I would also understand if you didn't want to add the CI step of docker build/docker push each time you release.

Thanks again.

[joellembatchou]

Hi,

We are currently only planning on publishing Docker images through Github.

Cheers,
Joelle

[akotlar]

Ah, I had checked your link on mobile, and the GitHub app just redirected me to the repo, so I though you were pointing out that you make the Dockerfile available Didn't know GitHub had this feature, cool. Thanks!

[akotlar]

This looks like it has a fairly important restriction. One needs to authenticate with Github before pulling the image. This makes docker pull ... break in a somewhat surprising way (authenticating to pull public image). Same issue is present when using as base image (FROM:)

edit: https://github.community/t/docker-pull-from-public-github-package-registry-fail-with-no-basic-auth-credentials-error/16358/18

Here's an example of a fairly large project running into issues with GitHub's image registry: containerd/containerd#3291 , even after providing credentials in some contexts.

[saphir746]

It's also not very compatible for use via Singularity

[matuskosut]

Hi @akotlar

I was working a little on publishing regenie in bioconda, which also includes docker images published to Biocontainers (https://biocontainers.pro/tools/regenie). It is an open community, so anyone can help out.

@saphir746 would Biocontainers work better with singularity?

[Shicheng-Guo]

Dear Joelle, any plan to update docker image to 3.0.3 ？

[joellembatchou]

You mean here:
https://github.com/rgcgithub/regenie/pkgs/container/regenie%2Fregenie/18094304?tag=v3.0.3.gz

[nathanweeks]

Hi @akotlar

I was working a little on publishing regenie in bioconda, which also includes docker images published to Biocontainers (https://biocontainers.pro/tools/regenie). It is an open community, so anyone can help out.

@saphir746 would Biocontainers work better with singularity?

@matuskosut @saphir746 A Singularity image created from the regenie Biocontainers image seems to work OK (#292)