Zero-configuration genomic data science with bioc2u

Author(s): Vincent James Carey,Alexandru Mahmoud

Affiliation(s): Channing Division of Network Medicine, Harvard Medical School



R/Bioconductor users on Linux platforms must often handle complex configuration tasks for packages that depend on runtime libraries completely external to R. Even when packages with compiled code are self-contained, source compilation can be time-consuming. The r2u system (https://github.com/eddelbuettel/r2u) produces Debian-style packages for all packages on CRAN. Installation of self-sufficient binaries is handled for Ubuntu 20.04 and 22.04 via the apt package manager, which is integrated with install.packages. This process has been extended to all Bioconductor software packages (https://github.com/bioconductor/bioc2u). We illustrate the use of this system for rapid configuration of 'naked' Linux systems and discuss its implications for container usage in scalable workflows.