The latest Terra-Jupyter-Bioconductor and R / Bioconductor Docker images are available in AnVIL and the Google Container Registry. They work like the bioconductor_docker images, with the capability to install almost all of the Bioconductor packages along with a few pre-installed “core” set of packages. The terra-jupyter-bioconductor image inherits from the terra-jupyter-r image which has all the system dependencies installed. This image has been tested on Leonardo and installs all but a few packages in Bioconductor release, which fail due to achived CRAN dependencies.
For the following images, check the CHANGELOG.md in their respective repositories for the most recent image URL.
The following image is available on the broad-dsp-gcr-public GCP Container Registry for terra-jupyter-bioconductor.
us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:{version} and can be used by selecting the “Bioconductor” notebook runtime. See the Terra-Jupyter-Bioconductor CHANGELOG.md.The following images are available on the anvil-gcr-public GCP Container Registry.
R / Bioconductor (release 3.14) is based on R version 4.1 and Bioconductor version 3.14. In Terra, it is listed with the version number as in us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:{version} and can be used by selecting a “custom” notebook runtime and selecting the RStudio image under “Community Maintained RStudio Environment (Verified Partners)”. See the AnVIL-RStudio-Bioconductor CHANGELOG.md.
R / Bioconductor (devel) In Terra, the image is accessible with the version number as in us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor-devel:{version}. It can be used by selecting “Other Environments”. See the AnVIL-RStudio-Bioconductor-devel CHANGELOG.md.
Legacy R / Bioconductor The image is based on R version 4.0.5 and Bioconductor version 3.13.