This repository provides scripts and documentation for an automated installation of research software and data resources.
For reproducibility and stability of the R software (and required libraries), a docker/singularity container is used. This enables to have parallel installation of different R versions and related R libraries.
Suggested containers for R are the official docker container(s) from Bioconductor, the bioconductor_docker images. These build on the official R/Posit containers and bundle an RStudio server version allowing thus interactive use of R through RStudio in a web browser. There is a docker image for each Bioconductor version (identified with the tag RELEASE_) ensuring thus reproducibility of analyses using a specific version of R and Bioconductor packages.
The docker containers can be pulled and installed using e.g. docker pull bioconductor/bioconductor_docker:RELEASE_3_22. Similarly, it is possible to
pull the docker image and convert to a singularity container using singularity pull docker://bioconductor/bioconductor_docker:RELEASE_3_22.
The Eurac Research Institute for Biomedicine defines its own container, building
on the Bioconductor container but adding additional libraries and software
required for some data analyses performed on study data. These are defined at
the
ifb_bioconductor_docker
GitHub repository and can be installed with e.g. docker pull jorainer/ifb_bioconductor_docker:RELEASE_3_22.
Along with R, also R libraries need to be installed. The sets of libraries are defined in txt files within the R sub-folder.