[Bioc-devel] bioconductor_docker updates

Turaga, Nitesh N|te@h@Tur@g@ @end|ng |rom Ro@we||P@rk@org
Mon Aug 3 18:30:15 CEST 2020

Hello Bioconductor Community,

A quick update about the latest developments on the Bioconductor Docker images.

We have updated the ‘devel’ image to inherit from the latest ‘rocker/rstudio:4.0.2’ image. This means that the `bioconductor/Bioconductor_docker:devel` image, which is now available will be running on,

  1.  Ubuntu 20.04
  2.  R version 4.0.2
  3.  Bioconductor version 3.12.

One major update to the system requirements was the installation of the ‘libglpk-dev’ which seemed to have caused issues installing the ‘igraph’ package. The version number of this image which can be queried through the docker command is going to be 3.12.13.

If you pull the updates from dockerhub using,

          docker pull bioconductor/Bioconductor_docker:devel

And check the version number using, (the result is going to be 3.12.13.

           docker inspect --format '{{ index .Config.Labels.version}}' bioconductor/bioconductor_docker:devel

NOTE: The release image stayed exactly the same but with the addition of the `libglpk-dev` package. The RELEASE_3_11 image did not get updated to Ubuntu 20.04. It is still based on Ubuntu 18.04. The devel image now works on a different version of Ubuntu (20.04) as compared to the build system (18.04. The support for the 18.04 image on rocker is no longer available.

The inspect label command for  RELEASE_3_11 (given below) should produce the new version number 3.11.11. Do not forget to pull. This is a bug fix with regards to the igraph package’s missing dependency.

docker inspect --format '{{ index .Config.Labels.version}}' bioconductor/bioconductor_docker:RELEASE_3_11

If you have any further questions, please reply to this thread.

Best regards,

Nitesh Turaga
Bioconductor Core Team

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