build your own singularity image

I was using the tidyverse rocker image on HPC by singularity pull. see my previous post. Everything was OK until I encountered problems installing jpeg and Cairo R packages. Later, I also had an error installing scRepertoire dependency gsl. It turns out I have to install debian packages inside the container: $ apt update && apt install -y –no-install-recommends libjpeg62-turbo-dev zlib1g-dev libpng-dev \ && apt install -y –no-install-recommends libx11-dev libcairo2-dev libxt-dev \ && apt install -y libgsl-dev However, singularity file system is read-only.

Run Rstudio server with singularity on HPC

Background Please read the following before go ahead: what is docker? what is Rocker? what is singularity? from Harvard Research computing website: Odyssey has singularity installed. Why Singularity? There are some important differences between Docker and Singularity: Docker and Singularity have their own container formats. Docker containers may be imported to run via Singularity. Docker containers need root privileges for full functionality which is not suitable for a shared HPC environment.