user-launcher-rstudio

#!/usr/bin/env bash
set -ue
thisdir="$(realpath -s "$(dirname "${BASH_SOURCE[0]}")")"

#
# Start the RStudio Server container where this folder is set as the 
# project directory by executing this file.
# 
# Use --help to print the help text.
#
# === Settings ===========================================================

# Edit this section to change the container options of this project. They
# are communicated to the container as environment variables. See the
# beginning of the scripts "rstudio" and "rstudio_adv" to see which 
# environment variables are expected.

# PROJECT_DIR:
# Per default this is set to the directory where this script lies.
PROJECT_DIR="$thisdir"

# BIND_PROJECT_TO:
# On which path the current folder will be visible inside the container
BIND_PROJECT_TO="/proj"

# EXTERNAL_FILES:
# Files/directories that are available in the container besides the project
# directory.
# The follwing example makes the directory /home/user/datasets available
# inside the container as "/ext/input", read-only:
#
#   "/home/user/datasets/:/ext/input:ro"  (including quotes)
#
# The first path must exist. The second path can be freely chosen.
# Omit ":ro" to enable write access from within the container.
# Separate multiple entries by newlines.
#
EXTERNAL_FILES=(
# "/home/user/datasets/:/ext/input:ro" 
)

# On which address and on which port range to start RStudio
ADDRESS="127.0.0.1"
PORT_MIN="8000"
PORT_MAX="8200"


# CONTAINER_DIR:
# Where the RStudio Server container is located (directory).
echo "Do not run this script directly, but use 'createproject-rstudio'" >&2; exit 1 ###REPLACE_HERE###


# ========= END OF SETTINGS ==================================================


# This section is for advanced modifications on how the container is started


# Find container no matter of $PWD and whether CONTAINER_DIR is relative or absolute
CONTAINER_DIR="$(cd "$thisdir"; realpath -s "$CONTAINER_DIR")"

# Path to the SIF file that is the container
CONTAINER="$CONTAINER_DIR/rstudio.sif"

# Path (host system) where the session data of different RStudio Server
# sessions is stored.  Per session, a subfolder is created that is mounted to
# ~/.rstudio inside the container.  Also, the .pid files are created here,
# holding information about network port, host machine and more.
DIR_RUN=".run"

# Further arguments to forward to "singularity instance start ..."
#   When the container is started without an instance (./rstudio exec 
#   without '-i' argument), ARGS_INSTANCE is also given to
#   singularity exec
ARGS_INSTANCE=(
  -H "$PROJECT_DIR:$BIND_PROJECT_TO"
)

# Further arguments to forward to "singularity exec ..."
ARGS_EXEC=(
  --cleanenv
)
# --cleanenv: Do not forward environment variables to the container. 
#   This is so that host variables like PYTHONPATH do not interfere
#   with the container. To set environment variables, add them to
#   .bash_profile. Or use --env-file or --env or prefix your environment
#   variable name with APPTAINERENV_ (formerly SINGULARITYENV_, see
#   Apptainer/Singularity help)

# forward the folders in EXTERNAL_FILES to Singularity
# idiom using "+" is necessary in case EXTERNAL_FILES is empty
for f in "${EXTERNAL_FILES[@]+"${EXTERNAL_FILES[@]}"}"; do
  ARGS_INSTANCE+=("-B" "$f")
done

# Parse the user arguments and launch the container 
# ========================================================

source "$CONTAINER_DIR/rstudio_adv"