GitHub - Bioconductor/bioc2u: Building containers and holding some code for bioc2u, an attempt at extending r2u to all bioc packages, and provide precompiled binaries for ubuntu systems (original) (raw)

Bioc2u (alpha): 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 only available for Ubuntu Jammy and is still in alpha development.

Getting started

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 aptand 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.shscript 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 bash

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 ther-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.

Done & TODOs (alpha)