This repository contains recipes for building singularity containers for various tasks, usually to run software on TSD that is difficult to install due to its being offline.

See subdirectories for the respective containers' descriptions.

Building singularity containers requires

1. A working singularity installation. I use a vagrant VM on macOS.
2. Sudo privileges.

Building is done with the build command, and requires a name of the container image you're building, and the path to a recipe. E.g.:

sudo singularity build r_container.simg r_container_with_deseq2.txt

It's also a good idea to reroute output messages from stdout to a log file. This makes it easier to find errors in the quite long stream of output, and can be done by piping the output to a file using tee:

sudo singularity build r_container.simg r_container_with_deseq2.txt | tee build_log.txt

To check if the built container works, e.g. that your R-packages have been installed correctly, you can run a shell in the container, open an R session and load the package:

singularity shell r_container.simg

then

R

and finally

library(DESeq2)