This project aims to extend r2u,
in hopes of providing a repository of Ubuntu binaries via apt for all Bioconductor packages.
Bioc2u is currently only available for Ubuntu Jammy and is still in alpha development.
If you wish to get started in a minimal environment, a relatively small docker container is provided, built on ubuntu:jammy, and providing the initial apt
and R setup to get you started. You may use this container via docker run --rm -it ghcr.io/bioconductor/bioc2u-user:jammy. Alternatively, if you are on
an Ubuntu machine, you may set up the bioc2u and r2u repositories for your local system's apt by using the provided script!
In an Ubuntu environment (tested in ubuntu:jammy container), 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.
# Install curl if missing
apt update -qq
apt install -y --no-install-recommends curl ca-certificates
# Run apt script
curl https://raw.githubusercontent.com/Bioconductor/bioc2u/devel/apt_setup.sh | sudo bashAfter 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.
By default, the r-core-base installation (provided by the r2u project), uses the bspm package to enable the usage of the package manager
when installing packages from within R via install.packages() or BiocManager::install(). You may thus continue to use R as you would outside of this
environment, and observe the speedup resulting from R using the apt package manager under the hood.
- Repository with signature hosted on Open Storage Network
- 3264 packages built for Bioconductor 3.18 and Ubuntu Jammy (software packages + dependent annotation/experiment packages)
- TODO: Formalize and publicize build process and failed packages