script.sh.erb

#!/usr/bin/bash -l
<% is_sofia = OodAppkit.clusters.any? { |c| c.id.to_s == "sofia" } %>
<%= ERB.new(File.read('../common_files/work_directory_change.sh.erb'), eoutvar: 'child').result(binding) %>

# Benchmark info
echo "TIMING - Starting main script at: $(date)"

# Set XDG_DATA_HOME to redirect the rstudio cache
if [[ -z "$XDG_DATA_HOME" ]]; then
    export XDG_DATA_HOME="<%= is_sofia ? '$HOME' : '$VSC_DATA' %>/.local/share"
    echo "setting XDG_DATA_HOME=$XDG_DATA_HOME"
fi

TOOLCHAIN=<%= context.toolchain %>

modules_to_load=()

case "${TOOLCHAIN}" in
  2022a )
    modules_to_load+=("RStudio-Server/2022.07.2+576-foss-2022a-Java-11-R-4.2.1")
    modules_to_load+=("R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1")
    ;;
  2023a )
    modules_to_load+=("RStudio-Server/2023.12.1+402-gfbf-2023a-Java-11-R-4.3.2")
    modules_to_load+=("R-bundle-Bioconductor/3.18-foss-2023a-R-4.3.2")
    ;;
  2024a )
    modules_to_load+=("RStudio-Server/2024.12.0+467-foss-2024a-R-4.4.2")
    modules_to_load+=("R-bundle-Bioconductor/3.20-foss-2024a-R-4.4.2")
    ;;
  2025a )
    modules_to_load+=("RStudio-Server/2025.09.2+418-foss-2025a-R-4.5.1")
    modules_to_load+=("R-bundle-Bioconductor/3.22-foss-2025a-R-4.5.1")
    ;;
  * )
    echo "ERROR: Unsupported toolchain selected"
    exit 1
    ;;
esac

module load "${modules_to_load[@]}"

# PAM auth helper used by RStudio
export RSTUDIO_AUTH="$OOD_SESSION_STAGED_ROOT/bin/auth"
export RSESSION_LOG_FILE="$OOD_SESSION_STAGED_ROOT/rsession.log"

<%- unless context.global_prerun.empty? -%>
<%= context.global_prerun.gsub("\r", "") %>
<%- end -%>

# System preferences at $RSTUDIO_CONFIG_DIR/rstudio-prefs.json (default location = /etc/rstudio)
# User preferences have priority over system preferences
export RSTUDIO_CONFIG_DIR="$OOD_SESSION_STAGED_ROOT/config_dir"

CLEAN_WORKSPACE=<%= context.clean_workspace %>
if [[ "${CLEAN_WORKSPACE}" == "no" ]]; then
    prefs_file=$RSTUDIO_CONFIG_DIR/rstudio-prefs.json
    prefs=$(<$prefs_file) && jq '.load_workspace = true' <<<$prefs >$prefs_file
fi

# write environment to a file.
export > "$OOD_SESSION_STAGED_ROOT/env.sh"

RSESSION_WRAPPER_SCRIPT="$OOD_SESSION_STAGED_ROOT/rsession.sh"
RSESSION_CONFIG="$OOD_SESSION_STAGED_ROOT/etc/rsession.conf"

# Launch the RStudio Server
echo "Starting up rserver on $HOSTNAME with password $RSTUDIO_PASSWORD for $USER"

$EBROOTRSTUDIOMINSERVER/bin/rserver \
  --rsession-path "${RSESSION_WRAPPER_SCRIPT}" \
  --rsession-config-file "${RSESSION_CONFIG}" \
  --www-port "${port}" \
  --auth-none 0 \
  --auth-pam-helper-path "${RSTUDIO_AUTH}" \
  --auth-encrypt-password 0 \
  --database-config-file "$OOD_SESSION_STAGED_ROOT/bin/database.conf" \
  --server-data-dir "/tmp/run-$USER" \
  --server-working-dir "$OOD_WD" \
  --server-user "$USER"