singularity_start.sh

#! /usr/bin/env bash

# project specific vars
export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"
export PROJECT_FOLDER="/projects/academic/adamw/"

# Run as particular group to use group storage
newgrp grp-adamw

# apptainer directories
export APPTAINER_CACHEDIR="/scratch/"$USER"/apptainer"
export SIF_PATH=$PROJECT_FOLDER"/users/"$USER"/apptainer"
export TMPDIR=$APPTAINER_CACHEDIR
export APPTAINER_TMPDIR=$APPTAINER_CACHEDIR

# set singularity cache and tmp directories to the same as apptainer
# needed because CCR is still using singularity and it will use these directories
export SINGULARITY_CACHEDIR=$APPTAINER_CACHEDIR
export SINGULARITY_TMPDIR=$APPTAINER_TMPDIR
export SINGULARITY_LOCALCACHEDIR=$APPTAINER_LOCALCACHEDIR

# path to singularity container file.  If you want to use a different image, you'll need
# to update this line.
export CONTAINER_PATH=$SIF_PATH/$SIF_FILE 

# to use for ssh:
export SERVER_URL="horae.ccr.buffalo.edu"

# Create the folders if they don't already exist
mkdir -p $APPTAINER_CACHEDIR/tmp
mkdir -p $APPTAINER_CACHEDIR/run
mkdir -p $APPTAINER_CACHEDIR/rstudio

# Start the instance using variables above
singularity instance start \
      --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
      --bind $APPTAINER_CACHEDIR/tmp:/tmp \
      --bind $APPTAINER_CACHEDIR/run:/run \
      --bind $APPTAINER_CACHEDIR/rstudio:/var/lib/rstudio-server \
      $CONTAINER_PATH rserver

# Start the rserver within the container
singularity exec instance://rserver rserver --server-user=$USER --www-port ${PORT} --auth-none=0 --auth-pam-helper-path=pam-helper &

# write a file with the details (port and password)
echo "
    1. SSH tunnel from your workstation using the following command:

       ssh -N -L 8787:${SERVER_URL}:${PORT} ${USER}@${SERVER_URL}

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

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

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

    3. to repeat these instructions:

      cat ~/singularity_status.txt


    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:

          singularity instance stop rserver


" > ~/singularity_status.txt

cat ~/singularity_status.txt