Container information

Name	RStudio
Description	This container is mainly for running RStudio (now Posit). The base image containging rstudio comes from the Rocker Project
URL/repo	https://github.com/rocker-org/rocker-versioned2
Version(s)	4.4.1, 4.5.1, 4.5.2
QUAY	https://quay.io/repository/cellgeni/rstudio

Singularity considerations

• ldap_auth file present in this repo allows to use LDAP authentication with RStudio instead of a custom password being setup. This requires the image to have the ldap3 python package installed. You still need to pass the username when launching rserver with --server-user.
• We also recommend using custom logging.conf to control verbosity.
• Some additional bindings are required to fully use rstudio and interact with LSF.
• Some of the paths inside the container will need to be writable, particularly the settings folders. In the example, <WORK_DIR> can be replaced with a folder you control. The bind on <WORK_DIR> shouldn't take much storage so it's fine to bind that to somewhere on your home folder.
• By default an rstudio folde will try to be created in /tmp. Because this may be a shared environment and to allow multiple users at the same time, in this example a custom bind is in place for that using /tmp/$(whoami)/rstudio
• <PORT> is an open port on the host you're launching RStudio. You can set PORT as an environment variable with the first open free port using this:

PORT=$(python3 -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')

• /path/to/rstudio.sif is the path to the singularity image built for rstudio on the filesystem.

Example

singularity exec \
    --pid \
    --bind /path/to/logging.conf:/etc/rstudio/logging.conf:ro \
    --bind /path/to/ldap_auth:/usr/lib/rstudio-server/bin/ldap_auth:ro \
    --bind /sys/fs/cgroup \
    --bind /etc/lsf.conf \
    --bind /usr/local/lsf \
    --bind <WORK_DIR>/keybindings:/etc/rstudio/keybindings \
    --bind <WORK_DIR>/run:/run \
    --bind /tmp/$(whoami)/rstudio:/tmp \
    --bind <WORK_DIR>/rstudio-server:/var/lib/rstudio-server \
    --bind /software,/nfs,/lustre \
    /path/to/rstudio.sif \
    rserver \
        --server-user $USER \
        --www-port <PORT> \
        --www-address 0.0.0.0 \
        --auth-none 0  \
        --auth-pam-helper-path ldap_auth