Merge branch 'main' into sofia-slicer

Author: JarneRenders

apps/code-server/template/script.sh.erb

@@ -1,4 +1,6 @@
 #!/usr/bin/bash -l
+<% is_sofia = OodAppkit.clusters.any? { |c| c.id.to_s == "sofia" } %>
+DATA_DIR="<%= is_sofia ? '$HOME' : '$VSC_DATA' %>"
 
 <%= ERB.new(File.read('../common_files/work_directory_change.sh.erb'), eoutvar: 'child').result(binding) %>
 
@@ -8,15 +10,17 @@ echo "TIMING - Starting main script at: $(date)"
 # Make symlinks for ~/.vscode and ~/.vscode-server
 for dir in .vscode .vscode-server; do
     if [[ ! -e ~/"$dir" ]]; then
-        mkdir -v -p "$VSC_DATA/$dir"
-        ln -v -s "$VSC_DATA/$dir" ~/"$dir"
+        mkdir -v -p "$DATA_DIR/$dir"
+<% unless is_sofia %>
+        ln -v -s "$DATA_DIR/$dir" ~/"$dir" # already at $HOME on sofia
+<% end %>
     fi
 done
 
 module load code-server
 
-extensions_dir="${VSC_DATA}/.config/code-server/extensions"
-data_dir="${VSC_DATA}/.config/code-server/data"
+extensions_dir="${DATA_DIR}/.config/code-server/extensions"
+data_dir="${DATA_DIR}/.config/code-server/data"
 
 mkdir -p "$extensions_dir"
 mkdir -p "$data_dir"

apps/code-tunnel/template/custom.sh.erb

@@ -1,10 +1,14 @@
 #!/bin/bash
+<% is_sofia = OodAppkit.clusters.any? { |c| c.id.to_s == "sofia" } %>
+DATA_DIR="<%= is_sofia ? '$HOME' : '$VSC_DATA' %>"
 
 # Make symlinks for ~/.vscode and ~/.vscode-server
 for dir in .vscode .vscode-server; do
     if [[ ! -e ~/"$dir" ]]; then
-        mkdir -v -p "$VSC_DATA/$dir"
-        ln -v -s "$VSC_DATA/$dir" ~/"$dir"
+        mkdir -v -p "$DATA_DIR/$dir"
+<% unless is_sofia %>
+        ln -v -s "$DATA_DIR/$dir" ~/"$dir" # already at $HOME on sofia
+<% end %>
     fi
 done
 
@@ -27,6 +31,7 @@ custom="$confdir/custom.conf"
 cat > $custom<<EOF
 new-session -d -s $TSES
 set -g status off #NOTE: this will disable the status bar (green text in the bottom)
+pipe-pane -o -t $TSES 'cat >> $OOD_SESSION_STAGED_ROOT/tunnel_session.log'
 EOF
 
 IFS=$'\n' # set the Internal Field Separator to newline

apps/code-tunnel/template/custom_commands.conf

@@ -1,6 +1,6 @@
 export VSCODE_CLI_USE_FILE_KEYCHAIN=1
 reset
 echo
-echo "Copy the device code, open the url and paste it to create the tunnel vsc-$USER-$(hostname -d | sed 's/.os$//')"
+echo "Copy the device code, open the url and paste it to create the tunnel vsc-$USER-$VSC_INSTITUTE_CLUSTER"
 echo
-code tunnel --accept-server-license-terms --name vsc-$USER-$(hostname -d | sed "s/.os$//")
+code tunnel --accept-server-license-terms --name vsc-$USER-$VSC_INSTITUTE_CLUSTER

apps/rstudio/form.yml.erb

@@ -7,9 +7,11 @@ attributes:
     widget: "select"
     options:
       - ["2025a: RStudio-Server/2025.09.2+418 + R/4.5.1", "2025a"]
+<% unless is_sofia %>
       - ["2024a: RStudio-Server/2024.12.0+467 + R/4.4.2", "2024a"]
       - ["2023a: RStudio-Server/2023.12.1+402 + R/4.3.2", "2023a"]
       - ["2022a: RStudio-Server/2022.07.2+576 + R/4.2.1", "2022a"]
+<% end %>
     help: |
       R-bundle-CRAN and R-bundle-Bioconductor are loaded by default.
   clean_workspace:

apps/rstudio/template/script.sh.erb

@@ -1,13 +1,13 @@
 #!/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 "$XDG_DATA_HOME" ]]; then
-    export XDG_DATA_HOME="$VSC_DATA/.local/share"
+    export XDG_DATA_HOME="<%= is_sofia ? '$HOME' : '$VSC_DATA' %>/.local/share"
     echo "setting XDG_DATA_HOME=$XDG_DATA_HOME"
 fi
 

apps/vub_desktop/template/script.sh.erb

@@ -5,9 +5,6 @@
 # Benchmark info
 echo "TIMING - Starting main script at: $(date)"
 
-# Set VGL_DISPLAY to a GPU card if available, otherwise to Mesa llvmpipe
-<%= ERB.new(File.read('../common_files/oodegl.sh.erb'), eoutvar: 'child').result(binding) %>
-
 <%- unless context.global_prerun.empty? -%>
 <%= context.global_prerun.gsub("\r", "") %>
 <%- end -%>
@@ -23,9 +20,13 @@ if [ -e $xfce_container ]; then
         --bind /run/munge \
         $xfce_container \
         bash -s << 'END'
+# Set VGL_DISPLAY to a GPU card if available, otherwise to Mesa llvmpipe
+<%= ERB.new(File.read('../common_files/oodegl.sh.erb'), eoutvar: 'child').result(binding) %>
 <%= ERB.new(File.read("../common_files/desktops/#{context.desktop}.sh.erb"), eoutvar: 'child').result(binding) %>
 END
 else
+# Set VGL_DISPLAY to a GPU card if available, otherwise to Mesa llvmpipe
+<%= ERB.new(File.read('../common_files/oodegl.sh.erb'), eoutvar: 'child').result(binding) %>
 <%= ERB.new(File.read("../common_files/desktops/#{context.desktop}.sh.erb"), eoutvar: 'child').result(binding) %>
 fi
 

files/ood/profile_sofia

@@ -15,8 +15,9 @@ if [ -n "$PUNUSER" ]; then
     # This only stops pun startup. Pre-existing puns should be cleaned in <2 hours via cron.
     logger -- "Checking whether $PUNUSER is in bsofia_projects and pun should be started"
     if [[ "$1" == "pun" ]] && ! id -Gn "$PUNUSER" 2>/dev/null | grep -qw 'bsofia_projects'; then
-        echo "Access denied: $PUNUSER is not authorized to use this system." >&2
-        echo "User $PUNUSER is not part of the bsofia_projects group." >&2
+        echo "Access denied: $PUNUSER is not a member of an active Tier-1 compute project on sofia." >&2
+        echo "Note that access to sofia is managed through the VSC hub, not the account.vscentrum.be account page." >&2
+        echo "See https://docs.vscentrum.be/brussel/tier1_sofia.html#getting-access for how to request or join a project." >&2
         echo "Please contact the support team (support@vscentrum.be) if you believe this is an error." >&2
         exit 1
     fi

ondemand-vub.spec

@@ -10,7 +10,7 @@ install -Dpm644 %{_datadir}/ondemand-vub/%1/ondemand.d/general_options.yml %{_sy
 
 Summary: Scripts, customizations and tools for Open OnDemand
 Name: ondemand-vub
-Version: 2.53
+Version: 2.55
 Release: 1
 BuildArch: noarch
 License: GPL
@@ -103,8 +103,13 @@ chmod 0750 %{_localstatedir}/www/ood/apps/sys/abaqus
 chmod 0000 %{_localstatedir}/www/ood/apps/sys/abaqus
 
 %changelog
-* Mon Jul 13 2026 Jarne Renders <jarne.thijs.renders@vub.be>
+* Thu Jul 63 2026 Jarne Renders <jarne.thijs.renders@vub.be>
 - Adapt slicer app for sofia
+* Thu Jul 16 2026 Jarne Renders <jarne.thijs.renders@vub.be>
+- Improve sofia access denied message with VSC hub instructions
+* Mon Jul 13 2026 Jarne Renders <jarne.thijs.renders@vub.be>
+- Adapt rstudio, code-tunnel and code-server apps for sofia
+- Add better logging for code-tunnel
 * Mon Jul 13 2026 Jarne Renders <jarne.thijs.renders@vub.be>
 - Load oodegl.sh inside VNC container on sofia
 * Mon Jul 06 2026 Jarne Renders <jarne.thijs.renders@vub.be>