Bioc2u (beta): Ubuntu Binaries for Bioconductor packages

This project aims to extend r2u, in hopes of providing a repository of Ubuntu binaries via apt for all Bioconductor packages.

Bioc2u is currently available for Ubuntu Jammy (22.04) and Noble (24.04) and is still in beta development.

Container Images

We provide two types of container images for different use cases:

• User containers (bioc2u-user): Minimal environment built on ubuntu:jammy or ubuntu:noble with R, BiocManager, and bioc2u/r2u repositories pre-configured
• Builder containers (bioc2u-builder): Extended environment based on r2u containers with additional build tools for package development

Available Tags

Container images are available with multiple tagging formats:

• Ubuntu version: jammy, noble
• Ubuntu version with R: jammy-r-4.4.2, noble-r-4.4.2
• Ubuntu version with Bioconductor: jammy-bioc-3.21, noble-bioc-3.21
• Full version: jammy-bioc-3.21-r-4.5.1, noble-bioc-3.21-r-4.5.0
• OS version: 22.04, 24.04 (corresponding to Ubuntu versions)
• OS version with R/Bioc: eg 22.04-r-4.5.1, 24.04-bioc-3.21, 24.04-bioc-3.21-r-4.5.1

Version Strategy and Backward Compatibility

This design allows for old versions to remain accessible by default, under the full tags. For example: when R 4.5.1 comes out, the containers tagged simply jammy-bioc-3.21 become jammy-bioc-3.21-r-4.5.1 but the previous container remains accessible under jammy-bioc-3.21-r-4.5.0. When containers get rebuilt within the same version, old containers can still be used via their hash in the ghcr.io/bioconductor/bioc2u-user@sha256:[hash] format.

This ensures reproducibility by allowing users to pin to specific versions or use the latest versions through the shorter tag names.

Getting started

Using Docker containers

For a minimal R environment with bioc2u pre-configured: ```bash

Ubuntu Jammy (22.04) - latest versions

docker run --rm -it ghcr.io/bioconductor/bioc2u-user:jammy

Ubuntu Noble (24.04) - latest versions

docker run --rm -it ghcr.io/bioconductor/bioc2u-user:noble

Specific Bioconductor/R versions for reproducibility

docker run --rm -it ghcr.io/bioconductor/bioc2u-user:jammy-bioc-3.21-r-4.5.0 ```

For package development with build tools: ```bash

Builder container with development tools

docker run --rm -it ghcr.io/bioconductor/bioc2u-builder:jammy ```

Local installation

In an Ubuntu environment (eg in containers based on ubuntu:jammy and ubuntu:noble), you may use the apt_setup.sh script which will set up the Bioc2u apt repository and install R, and basic packages such as BiocManager. This script leverages the r2u setup scripts from the r2u repository to configure the CRAN apt repository.

```bash

Install curl if missing

apt update -qq apt install -y --no-install-recommends curl ca-certificates

Run apt script with specific Bioconductor version

curl https://raw.githubusercontent.com/Bioconductor/bioc2u/devel/apt_setup.sh | sudo bash -s 3.21 ```

After the initial setup, you may use apt or install.packages() freely. Installing packages through apt can be done in any shell session, by using the r-bioc- prefix and the all-lowercase name of the package, eg apt install -y r-bioc-genomicranges. You may alternatively continue to use R traditionally, as you would in any other environment, and observe the speedup resulting from R using the apt package manager under the hood.

Automated Builds

Container images are automatically built every 2 days and pushed to GitHub Container Registry (GHCR). The build process:

• Builds both user and builder containers for Ubuntu Jammy and Noble
• Supports linux/amd64 platform
• Automatically extracts R and OS version information for comprehensive tagging
• Creates multi-platform manifests with various tag combinations

Acknowledgments

This project builds upon and extends the r2u project. Our apt_setup.sh script directly uses the r2u setup scripts to configure the CRAN apt repository, and our builder containers are based on the r2u containers.