RStudio Server

Quick Start Guide

Example SLURM Script to launch RStudio Server:

User needs to set the following before starting script:

--mail-user=
--chdir=

R_LIBS_USER in ~/.Renviron. Example:

cat ~/.Renviron 
# Set local library installation path
R_LIBS_USER=/gscratch/srlab/${USER}/R_libs_singularity

After submitting script, view the SLURM output file located in --chdir= for information on:
1. How to create tunnel to Mox node.
2. What address to direct your web browser to.
3. Username/password to enter into RStudio Server interface.
4. How to terminate RStudio Server and the SLURM job.
Example script uses the following Singularity container image: rstudio-4.0.2.sjw-v1.0.

#!/bin/bash
## Job Name
#SBATCH --job-name=rstudio_server_test
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=0-08:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --signal=USR2
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=
## Specify the working directory for this job
#SBATCH --chdir=


################################################################
# Set user-defined variables inside this box.

# Set container path
container_path="/gscratch/srlab/programs/singularity_containers"

# Set container name
container="rstudio-4.0.2.sjw-v1.0.sif"
################################################################

## MAKE NO CHANGES BELOW THIS LINE

module load singularity



export PASSWORD=$(openssl rand -base64 15)
# get unused socket per https://unix.stackexchange.com/a/132524
# tiny race condition between the python & singularity commands
readonly PORT=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')
cat 1>&2 <<END
1. SSH tunnel from your workstation using the following command:

   ssh -N -L 8787:${HOSTNAME}:${PORT} ${USER}@mox.hyak.uw.edu

   and point your web browser to http://localhost:8787

2. log in to RStudio Server using the following credentials:

   user: ${USER}
   password: ${PASSWORD}

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f ${SLURM_JOB_ID}
END


##NOTE##
# This is a local drive location I can write, you should be able
# to just set to a subfolder of your HPC home/scratch directory
export TMPDIR="/gscratch/scrubbed/${USER}/rstudio-tmp"

mkdir -p "$TMPDIR/tmp/rstudio-server"
uuidgen > "$TMPDIR/tmp/rstudio-server/secure-cookie-key"
chmod 0600 "$TMPDIR/tmp/rstudio-server/secure-cookie-key"

mkdir -p "$TMPDIR/var/lib"
mkdir -p "$TMPDIR/var/run"

# User-installed R packages go into their home directory
if [ ! -e ${HOME}/.Renviron ]
then
  printf '\nNOTE: creating ~/.Renviron file\n\n'
  echo 'R_LIBS_USER=~/R/%p-library/%v' >> ${HOME}/.Renviron
fi

# This example bind mounts the /gscratch/scrubbed/${USER} directory on the host into the Singularity container.
# By default the only host file systems mounted within the container are $HOME, /tmp, /proc, /sys, and /dev.
singularity exec \
--bind="$TMPDIR/var/lib:/var/lib/rstudio-server" \
--bind="$TMPDIR/var/run:/var/run/rstudio-server" \
--bind="$TMPDIR/tmp:/tmp" \
--bind=/gscratch/scrubbed/${USER} \
${container_path}/${container} \
rserver --www-port ${PORT} --auth-none=0 --auth-pam-helper-path=pam-helper

Create/customize your own Singularity Rstudio Server container

NOTE: These instructions are written to be performed on Mox (Hyak).

Create a Singularity definition file:

Example filename: rstudio-4.0.2.sjw-v1.0.def
Here's an example with a good set of basic installations for R 4.0.2:

Bootstrap: docker
From: rocker/rstudio:4.0.2
%files
    # Load file with R package installation commands in to container at /tmp
    # Expects file called "r_packages_installs.R" to be in current directory.
    r_packages_installs.R /tmp/

%post
    # Install additinoal system packages in container
    # Most are needed for R/RStudio dependencies
    apt -y update
    apt -y install libxml2 libz-dev libbz2-dev liblzma-dev libxtst6 libxt6

    # Run R package installation script file
    Rscript /tmp/r_packages_installs.R

Create file r_packages_installs.R containing R package installation instructions.

NOTE: The container already has a base set of R packages (e.g. ggplot2 installed).
Here's an example with a set of commonly used packages:

# Update base packages
update.packages(ask = FALSE)

# Install BioConductor package manager
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.14")

# Install tidyverse
install.packages("tidyverse")

# Install matrixStats 0.61.0 (needed for DESeq2)
install.packages("https://cran.rstudio.com/src/contrib/matrixStats_0.61.0.tar.gz", repos=NULL, type="source")

# Install remotes package (allows for package installs from GitHub)
BiocManager::install("remotes")

# Install GSEABase (a dependency for numerous gene ontology/enrichment analysis)
BiocManager::install("Bioconductor/GSEABase")

# Install qvalue package
BiocManager::install("qvalue")

# Install GO.db (annotation maps for Gene Ontology data)
BiocManager::install("GO.db")

# Install MatrixGenerics (needed for DESeq2)
BiocManager::install("MatrixGenerics")

# Install Methylkit
BiocManager::install("methylKit")

# Install GOseq
BiocManager::install("goseq")

# Install WGCNA
BiocManager::install("WGCNA")

# Install DESeq2
BiocManager::install("DESeq2")

Log into a build node.
Load the Singularity module:

module load singularity
Build the container:
- NOTE: Container name will be rstudio-4.0.2.sjw-v1.0.sif
singularity build --fakeroot rstudio-4.0.2.sjw-v1.0.sif rstudio-4.0.2.sjw-v1.0.def
Use the SLURM script above.
- NOTE: Be sure to update the script line to reflect your container name:
```
# Set container name
container="rstudio-4.0.2.sjw-v1.0.sif"
```