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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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Tagged release OSCA docker images #58

Closed matthewcarlucci closed 3 years ago

matthewcarlucci commented 3 years ago

The bioconductor_docker container maintains tagged releases in parallel to the package releases. Is it possible to start pushing inherited tagged builds for bioconductor/orchestratingsinglecellanalysis to allow future reproducibility of the book and any derived works? I believe this should be as simple as:

  1. On RELEASE_3_12, increment the bioconductor_docker tag to RELEASE_3_12.
  2. Build as bioconductor/orchestratingsinglecellanalysis:RELEASE_3_12.
  3. Push this tagged build to DockerHub.

It seems this is the intended release practice for Bioconductor images based on https://github.com/Bioconductor/bioconductor_docker/blob/master/best_practices.md.

A build of the Dockerfile modification above appears to work. Please let me know if there is anything further I could do to help (PR to relevant branches?).

LTLA commented 3 years ago

We could do that, but speaking of the future, we have migrated to a new architecture at https://github.com/OSCA-source/OSCA. So there would need to be a bit of thought as to where the Dockerfile will live and how it would manage the install.

LTLA commented 3 years ago

It is done. 

docker pull bioconductor/orchestratingsinglecellanalysis:RELEASE_3_12

Note that latest is now somewhat different if you were previously relying on the location of the Rmarkdown files. The R packages should be still the same (more-or-less) so if you just needed the environment, you shouldn't have to worry.

matthewcarlucci commented 3 years ago

This appears to be working perfectly for my use case of reproducibly executing code derived from (i.e. code not present in the image itself) the version 3.12 book content, thank you!