The HPC was not allowed to use Docker, to facilitate the uniformity of running environment with R and rmats-turbo, I built the running environment with Dockerfile and pushed it to Docker Hub with GitHub Actions. Then pull the image from Docker Hub and run it with Singularity.

Use Singularity with non-privileged user

Install Go

# Install go
cd ~/tools
wget https://go.dev/dl/go1.17.5.linux-amd64.tar.gz
tar -xvf go1.17.5.linux-amd64.tar.gz
echo "export PATH=${HOME}/tools/go/bin/:\${PATH}" >> ~/.bashrc
source ~/.bashrc

Install Singularity from CE source

cd ~/tools
wget https://github.com/sylabs/singularity/releases/download/v3.9.2/singularity-ce-3.9.2.tar.gz
tar -xvf singularity-ce-3.9.2.tar.gz
cd singularity-ce-3.9.2
./mconfig --without-suid --prefix=${HOME}/tools/singularity-ce-3.9.2 && \
    make -C ./builddir && \
    make -C ./builddir install
echo "export PATH=${HOME}/tools/singularity-ce-3.9.2/bin/:\${PATH}" >> ~/.bashrc
source ~/.bashrc

Use jrocker/rstudio in Singularity

singularity pull docker://chunjiesamliu/jrocker:latest
mkdir -p run var-lib-rstudio-server

printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf

PASSWORD="🙃" singularity exec --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf rstudio_4.0.4.sif rserver --auth-none=0  --auth-pam-helper-path=pam-helper --auth-timeout-minutes=0 --auth-stay-signed-in-days=30

Pointing your browser to http://hostname:8787, enter your local user ID on the system as the username, and the custom password specified in the PASSWORD environment variable.

Use jrocker/rstudio in Singularity with Slurm

Slurm job script

#!/usr/bin/env bash
#SBATCH --time=08:00:00
#SBATCH --signal=USR2
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=8192
#SBATCH --output=/home/%u/tmp/errout/jrocker.job.%j
# customize --output path as appropriate (to a directory readable only by the user!)

# Create temporary directory to be populated with directories to bind-mount in the container
# where writable file systems are necessary. Adjust path as appropriate for your computing environment.
workdir=$(python -c 'import tempfile;from pathlib import Path; print(tempfile.mkdtemp(prefix="jrocker_", dir=str(Path.home()/"tmp/tmp")))')

mkdir -p -m 700 ${workdir}/run ${workdir}/tmp ${workdir}/var/lib/rstudio-server
cat > ${workdir}/database.conf <<END
provider=sqlite
directory=/var/lib/rstudio-server
END

# Set OMP_NUM_THREADS to prevent OpenBLAS (and any other OpenMP-enhanced
# libraries used by R) from spawning more threads than the number of processors
# allocated to the job.
#
# Set R_LIBS_USER to a path specific to rocker/rstudio to avoid conflicts with
# personal libraries from any R installation in the host environment

cat > ${workdir}/rsession.sh <<END
#!/usr/bin/env bash
export OMP_NUM_THREADS=${SLURM_JOB_CPUS_PER_NODE}
export R_LIBS_USER=${HOME}/R/jrocker
exec rsession "\${@}"
END

chmod +x ${workdir}/rsession.sh

export SINGULARITY_BIND="${workdir}/run:/run,${workdir}/tmp:/tmp,${workdir}/database.conf:/etc/rstudio/database.conf,${workdir}/rsession.sh:/etc/rstudio/rsession.sh,${workdir}/var/lib/rstudio-server:/var/lib/rstudio-server,/scr1/users/liuc9:/scr1/users/liuc9,/mnt/isilon/xing_lab/liuc9:/mnt/isilon/xing_lab/liuc9"

# Do not suspend idle sessions.
# Alternative to setting session-timeout-minutes=0 in /etc/rstudio/rsession.conf
# https://github.com/rstudio/rstudio/blob/v1.4.1106/src/cpp/server/ServerSessionManager.cpp#L126
export SINGULARITYENV_RSTUDIO_SESSION_TIMEOUT=0

export SINGULARITYENV_USER=$(id -un)
export SINGULARITYENV_PASSWORD=$(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} ${SINGULARITYENV_USER}@hpc

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

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

   user: ${SINGULARITYENV_USER}
   password: ${SINGULARITYENV_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

singularity exec --cleanenv ${HOME}/sif/jrocker_latest.sif \
    rserver --www-port ${PORT} \
            --auth-none=0 \
            --auth-pam-helper-path=pam-helper \
            --auth-stay-signed-in-days=30 \
            --auth-timeout-minutes=0 \
            --rsession-path=/etc/rstudio/rsession.sh
printf 'rserver exited' 1>&2