Fast-package installation with Bioconductor package binaries
Nitesh Turaga Dana Farber Cancer Institute
A container image is a standalone, executable software package that includes everything needed to run the software: a runtime, system tools, system libraries, and settings. Bioconductor provides the ‘bioconductor_docker’ container with an RStudio front end and all the system dependencies of Bioconductor packages as a containerized application. Bioconductor has provided this container image since release 3.10, as well as the current development version for developers to build and test their new packages.
A new addition to the Bioconductor container family is the availability of Bioconductor package binaries. These package binaries are now available Bioconductor for the current release and development branches of Bioconductor. These binaries add tremendous value to the container ecosystem in ‘fast package installation’ by removing the compilation step. They speed up continuous integration tools for developers to build and check packages during development.
Analysis using the RStudio interactive environment on cloud platforms like the AnVIL (www.anvilproject.org) become faster as these package binaries are available to any docker image that inherit from the ‘bioconductor_docker’ image.
This software demo showcases fast package installation using the package binaries on the ‘bioconductor_docker’ images and the AnVIL RStudio interactive environment.
Keywords: binary package installation,AnVIL,containers