3. Setup Singularity

Download The Singularity Image

The Singularity image may be downloaded from Singularity Hub by users without sudoer rights by running the following:

singularity pull --name rserver-launcher-centos7.simg shub://OSC/centos7-launcher

This will download the pre-built image to the current working directory.

Alternatively, Build The Singularity Image

Running a build is trivial but does require sudoer access to the build host.

Where Singularity is the file that defines the image. The image is basic, installing only the command which over the base CentOS 7 packages. This simplicity is because most of the actual executables and libraries must be bound and mounted into the container/guest at runtime from the host. By bind-mounting executables and libaries from the host system we are able to swap RStudio versions at launch time without having to update the Singuarlity image.

Likewise the runscript defined in the image uses the host $PATH which is propagated into the guest’s environment as $USER_PATH.

An example Singularity file for running RStudio:

Bootstrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum

  Maintainer OSC Gateways

This will run RStudio Server which must be mounted with dependencies into the container

%apprun rserver
  if ! [[ "$USER_PATH" = "" ]]; then
    export PATH="$USER_PATH"

  exec rserver "${@}"

  if ! [[ "$USER_PATH" = "" ]]; then
    export PATH="$USER_PATH"

  exec rserver "${@}"

yum install -y which