Bioconductor/bioconductor_docker

Update `latest` version to be the same as `RELEASE_3_13`

nuno-agostinho opened this issue · 5 comments

nuno-agostinho commented

Looking at bioconductor/bioconductor_docker in DockerHub, we can see a discrepancy between push dates for different image versions:

  • latest was last pushed 5 months ago (and still contains Bioconductor 3.12)
  • RELEASE_3_13 was pushed 16 hours ago
  • RELEASE_3_12 was released 1 month ago (so latest isn't even up-to-date compared to RELEASE_3_12...)

I always use the latest tag but it needs to be kept updated with the others. Could the latest tag somehow be automatically built to avoid such issues in the future? Thank you!

nturaga commented

Done.

nuno-agostinho commented

Thank you!! 😊

bschilder commented

Could the latest tag somehow be automatically built to avoid such issues in the future?

Was this ever implemented?

nturaga commented

IMHO the latest tag doesn't do us any favors. I'm debating just removing it completely and forcing people to use the specific RELEASE_X_Y tag or devel.

This is to keep things in line with what we do in R for Bioconductor. There is no "latest" version tag for Bioconductor.

I'm open to suggestions. I know a GitHub action can automate the process.

bschilder commented

Thanks for the explanation @nturaga !

Keeping a latest tag (or release in keeping with Bioc's naming) would be great with automated GHA, but I agree it's currently a bit confusing during those in-between periods.

I actually just put together some GHA workflows for automatically generating new Docker containers and pushing them to DockerHub. Something along these lines might be useful.
https://github.com/neurogenomics/r_workflows

A couple of additional modifications would need to be made:

  • In addition to triggering GHA with pushes, you could schedule daily checks to see if there's been any changes in the version of Bioconductor "devel" (or "release").
  • In the Dockerfile, change the base container: FROM rocker/rstudio:devel
  • Add the linux Dependencies not explicitly declared to the Dockerfile.
  • 👍1