New projects, packages, ideas for follow ups, new revisions, etc.

[nuest]

The paper is "finished", but if we really follow up with a CRAN Task View Containerisation, then we can keep the collection of container-related works up to date. Let's collect "new" packages and projects or things we missed in the article here, until we know where to publish them.

[nuest]

• docknitr: Using Docker in Rmarkdown to run chunks - https://cran.r-project.org/web/packages/docknitr/vignettes/docknitr.html

[nuest]

• mention BioContainers as source for base images: https://biocontainers.pro/#/ - via this Tweet and potentially involve @ypriverol

[nuest]

Rule 11 by Kovačević

COPY Dockerfile /

Via https://twitter.com/kovmil/status/1326334135896518661

@kovmil I'll think about this a little bit more, but my spontaneous reaction is: it would have been great you'd seen the preprint!

[kovmil]

Will most definitely do! And yeah, copying the Dockerfile to the image's root folder can do wonders with Dockerfile code reuse.

[nuest]

Screenshot from https://journals.plos.org/ploscompbiol/article/comment?id=10.1371/annotation/d538b698-fbf5-4318-8e45-c421d2495b8c

• Mentions option to freeze whole APT repositories to a specific date, e.g. http://neuro.debian.net/pkgs/neurodebian-freeze.html - I think this is indeed a god option
• Mentions https://github.com/ReproNim/neurodocker/ as a tool, though I would have the concern here that neurodocker is a CLI tool to generate a Dockerfile, which might not be accessible to many users, but it allows to enforce good practices within the generated Dockerfile
• Mentions https://github.com/datalad/datalad-container/ and git-annex - would have to look more closely, first reaction would be that git-annex goes to far for the target audience, but is could be a nice way to snapshot/version control the actual exported image

[bdevans]

There are some interesting ideas here! I noticed that there are some highlights/comments on the OSF preprint too. It might be worth keeping an eye on that for more useful suggestions.

[sje30]

Good to see our friend Yaroslav contributing some great points!

On Wed, Nov 25 2020, Daniel Nüst wrote:

Screenshot from https://journals.plos.org/ploscompbiol/article/comment?id=10.1371/annotation/d538b698-fbf5-4318-8e45-c421d2495b8c

• Mentions option to freeze whole APT repositories to a specific date, e.g. http://neuro.debian.net/pkgs/neurodebian-freeze.html - I think this is indeed a god option
• Mentions https://github.com/ReproNim/neurodocker/ as a tool, though I would have the concern here that neurodocker is a CLI tool to generate a Dockerfile, which might not be accessible to many users, but it allows to enforce good practices within the generated Dockerfile
• Mentions https://github.com/datalad/datalad-container/ and git-annex - would have to look more closely, first reaction would be that git-annex goes to far for the target audience, but is could be a nice way to snapshot/version control the actual exported image

[vsoch]

All hail @yarikoptic!

[yarikoptic]

Great to see my humble comments to the great paper are taken into consideration ;) we also have WiP script to help to backup all docker images for a repository into git-annex (well -- datalad-container extension) for posterity/backup/re-sharing/whatever

[nuest]

https://uwekorn.com/2021/03/03/deploying-conda-environments-in-docker-cheatsheet.html

(via https://twitter.com/xhochy/status/1367194297330786311?s=09)