Add Remote Desktop app (XFCE + Fiji via noVNC)

.github/workflows/build-desktop.yml

@@ -0,0 +1,51 @@
+name: Build desktop image
+
+on:
+  push:
+    tags: ["desktop-v*"]
+  pull_request:
+    paths:
+      - "desktop/**"
+      - ".github/workflows/build-desktop.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+env:
+  IMAGE: ghcr.io/janeliascicomp/fg-interactive-apps/desktop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GHCR
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Compute image tags
+        id: tags
+        run: |
+          if [[ "$GITHUB_REF" == refs/tags/desktop-v* ]]; then
+            version="${GITHUB_REF_NAME#desktop-v}"
+            echo "tags=${IMAGE}:${version},${IMAGE}:latest" >> "$GITHUB_OUTPUT"
+          else
+            echo "tags=${IMAGE}:dev" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Build (and push, except on pull requests)
+        uses: docker/build-push-action@v6
+        with:
+          context: desktop
+          platforms: linux/amd64
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.tags.outputs.tags }}

README.md

@@ -9,6 +9,7 @@ Each app lives in its own subdirectory with its own `runnables.yaml` manifest. F
 | App | Directory | Description |
 |-----|-----------|-------------|
 | **OpenVSCode** | [`vscode/`](vscode/) | Browser-based VS Code IDE ([openvscode-server](https://github.com/gitpod-io/openvscode-server)) running in an Apptainer container, with one-click tokenized access. |
+| **Remote Desktop** | [`desktop/`](desktop/) | Full Linux desktop (XFCE) with [Fiji](https://fiji.sc/) preinstalled, streamed to the browser via VNC/noVNC from an Apptainer container. |
 | **JupyterLab** | [`jupyterlab/`](jupyterlab/) | JupyterLab notebook server (SciPy stack) running in an Apptainer container. |
 | **marimo** | [`marimo/`](marimo/) | [marimo](https://marimo.io/) reactive Python notebook server running in an Apptainer container. |
 | **TensorBoard** | [`tensorboard/`](tensorboard/) | [TensorBoard](https://www.tensorflow.org/tensorboard) training-log dashboard running in an Apptainer container. |

desktop/Dockerfile

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+# Browser-accessible XFCE desktop with Fiji, for the Fileglancer Remote
+# Desktop app. Runs read-only under rootless Apptainer on cluster nodes: no
+# systemd/s6, nothing writes inside the image at runtime, and everything is
+# started by /opt/fg-desktop/start-desktop.sh as the (non-root) invoking user.
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8
+
+# Desktop + VNC stack, plus the X/GL/font libraries Fiji (Java Swing) needs.
+# --no-install-recommends keeps the image lean and, importantly, keeps screen
+# lockers (light-locker/xfce4-screensaver) out: a locked screen inside the
+# container could never be unlocked.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        xfce4 \
+        xfce4-terminal \
+        elementary-xfce-icon-theme \
+        dbus-x11 \
+        xauth \
+        x11-xserver-utils \
+        tigervnc-standalone-server \
+        python3 \
+        python3-pip \
+        ca-certificates \
+        curl \
+        unzip \
+        fonts-dejavu-core \
+        fontconfig \
+        libxext6 \
+        libxrender1 \
+        libxtst6 \
+        libxi6 \
+        libxrandr2 \
+        libgl1 \
+        libglu1-mesa \
+    && rm -rf /var/lib/apt/lists/*
+
+# websockify >= 0.11 provides the UnixDomainSocketDirectory token plugin that
+# the launcher's security model depends on; assert it imports at build time.
+RUN pip3 install --no-cache-dir --break-system-packages websockify==0.13.0 \
+    && python3 -c 'from websockify.token_plugins import UnixDomainSocketDirectory'
+
+# noVNC browser client (static files only; websockify does the serving)
+ARG NOVNC_VERSION=1.6.0
+RUN curl -fsSL "https://github.com/novnc/noVNC/archive/refs/tags/v${NOVNC_VERSION}.tar.gz" \
+        | tar -xz -C /opt \
+    && mv "/opt/noVNC-${NOVNC_VERSION}" /opt/novnc
+
+# Fiji, with bundled JDK. Only a rolling "latest" bundle is published these
+# days (the versioned releases/ directory stopped at 2.14.0 in 2023), so
+# reproducibility comes from this image's version tag, not the Fiji URL.
+RUN curl -fsSL https://downloads.imagej.net/fiji/latest/fiji-latest-linux64-jdk.zip \
+        -o /tmp/fiji.zip \
+    && unzip -q /tmp/fiji.zip -d /tmp/fiji-extract \
+    && rm /tmp/fiji.zip \
+    && d="$(find /tmp/fiji-extract -mindepth 1 -maxdepth 1 -type d)" \
+    && mv "$d" /opt/fiji \
+    && rmdir /tmp/fiji-extract \
+    && { test -x /opt/fiji/fiji-linux-x64 \
+         || test -x /opt/fiji/ImageJ-linux64 \
+         || test -x /opt/fiji/fiji; }
+
+COPY fiji-wrapper.sh /usr/local/bin/fiji
+COPY fiji.desktop /usr/share/applications/fiji.desktop
+COPY start-desktop.sh /opt/fg-desktop/start-desktop.sh
+RUN chmod 755 /usr/local/bin/fiji /opt/fg-desktop/start-desktop.sh
+
+CMD ["/opt/fg-desktop/start-desktop.sh"]

desktop/README.md

@@ -0,0 +1,48 @@
+# Remote Desktop
+
+Runs a full Linux desktop (XFCE) with [Fiji](https://fiji.sc/) preinstalled on a cluster node as a Fileglancer **service**, streamed to your browser with VNC ([TigerVNC](https://tigervnc.org/) + [noVNC](https://novnc.com/)), entirely inside an [Apptainer](https://apptainer.org/) container. The only host requirement is Apptainer.
+
+Your home directory is bind-mounted and writable, so files, XFCE settings, and anything you save persist across sessions. An optional **Data Folder** parameter bind-mounts an additional file-share folder and links it on the desktop.
+
+## One-click access
+
+Fileglancer mints a per-session secret (`$FG_SERVICE_TOKEN`) and publishes the service URL with the token embedded (`?path=websockify%3Ftoken%3D...`) once the server is ready, so clicking **Open Service** drops you straight onto the desktop — no password prompt. The desktop auto-resizes to fit your browser window (`resize=remote`).
+
+## Security model
+
+The session is protected at every hop, including against other users on the same shared compute node:
+
+- **Network**: the only listener is websockify on the Fileglancer-provided port. It serves the noVNC page to anyone, but only tunnels WebSocket connections that present the correct per-job 192-bit token.
+- **VNC server**: Xvnc listens **only on a unix domain socket** in a mode-0700 node-local directory (`-rfbport -1` disables TCP entirely). The socket file is named after the token, and websockify's `UnixDomainSocketDirectory` token plugin maps token → socket, so a wrong token matches nothing and local users cannot reach the VNC server at all — the kernel enforces the directory permissions.
+- **X display**: the X server requires an xauth cookie (mode 0600), so other local users cannot attach to the display through `/tmp/.X11-unix`.
+- The token never appears on a command line (only the socket *directory* does), so it cannot leak via `ps`.
+
+**Caveats**: anyone with the tokenized URL gets the full desktop, including a terminal running as you, while the job runs — treat the URL as a secret and stop the service when finished. Traffic between your browser and the compute node is plain HTTP (unencrypted), the same trade-off as the other apps in this repository.
+
+## How it works
+
+- The image (`ghcr.io/janeliascicomp/fg-interactive-apps/desktop`) is pulled to your per-user Apptainer cache on first launch and reused afterwards. It is large (several GB), so the first launch takes a while — Fileglancer shows the "pulling image" phase during the wait.
+- `start-desktop.sh` finds a free X display, starts Xvnc on a private unix socket with an xauth cookie, launches an XFCE session over D-Bus, and serves noVNC/websockify on `$FG_SERVICE_PORT` in the foreground — stopping the job tears everything down.
+- Fiji lives at `/opt/fiji` inside the read-only image, with a launcher on the desktop and in the applications menu.
+
+## Fiji notes
+
+- The image install is **read-only**, so the ImageJ updater cannot add plugins or update sites there (automatic update checks are disabled). To use custom plugins/update sites, unpack your own Fiji into your home directory — it persists across sessions and appears in the same desktop.
+- Fiji is refreshed to the then-current release whenever a new image version is built; pin behavior by keeping the `container:` tag in `runnables.yaml` at a version you have validated.
+
+## Parameters
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| **Data Folder** | directory | — | Optional folder to show on the desktop. Must be within a mounted file share; bind-mounted into the container automatically. Your home directory is always available. |
+
+## Building and releasing the image
+
+The image is built by the [`build-desktop`](../.github/workflows/build-desktop.yml) GitHub Actions workflow. Pull requests touching `desktop/` get a validation build; pushing a tag like `desktop-v1.0.0` builds and publishes `ghcr.io/janeliascicomp/fg-interactive-apps/desktop:1.0.0` (and `:latest`).
+
+After the first publish, set the GHCR package visibility to **public** (GitHub → org → Packages → `fg-interactive-apps/desktop` → settings) so Apptainer on the cluster can pull it anonymously. Then update the `container:` tag in `runnables.yaml` to match.
+
+## Notes
+
+- **Walltime** defaults to `08:00`. The desktop runs until you stop it or the walltime expires — raise it for longer sessions.
+- Resolution defaults to 1920x1080 before the first browser connect; after that the desktop follows your browser window size.

desktop/fiji-wrapper.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+# Launch Fiji from the read-only image install at /opt/fiji.
+#
+# The image is immutable under Apptainer, so the ImageJ updater cannot modify
+# this install; automatic update checks are disabled below. Users who need
+# extra plugins or update sites can unpack their own Fiji into $HOME (which
+# persists across sessions) and run it from there instead.
+for exe in /opt/fiji/fiji-linux-x64 /opt/fiji/ImageJ-linux64 /opt/fiji/fiji; do
+  if [ -x "$exe" ]; then
+    exec "$exe" -Dimagej.updater.disableAutocheck=true "$@"
+  fi
+done
+echo "ERROR: no Fiji launcher found in /opt/fiji" >&2
+exit 1

desktop/fiji.desktop

@@ -0,0 +1,9 @@
+[Desktop Entry]
+Type=Application
+Name=Fiji
+Comment=Fiji is just ImageJ - image processing and analysis
+Exec=fiji %F
+Icon=/opt/fiji/images/icon.png
+Terminal=false
+Categories=Science;ImageProcessing;Graphics;
+StartupNotify=true

desktop/runnables.yaml

@@ -0,0 +1,37 @@
+name: Remote Desktop
+description: Run a full Linux desktop (XFCE) with Fiji preinstalled on a cluster node, via Apptainer.
+requirements:
+    - apptainer
+
+runnables:
+    - id: serve
+      name: Desktop
+      type: service
+      description: >-
+          Start an XFCE desktop with Fiji preinstalled and open it in your
+          browser. Your home directory is mounted and writable. Runs until
+          you stop it.
+      # Fileglancer publishes the service URL once the port is live (auto_url)
+      # and embeds the token it minted ($FG_SERVICE_TOKEN) via
+      # service_url_suffix, so "Open Service" connects in one click. Inside
+      # the container, websockify only tunnels WebSocket connections whose
+      # ?token= names the VNC unix socket in a private 0700 directory; see
+      # start-desktop.sh for the full security model.
+      auto_url: true
+      service_url_suffix: "/vnc.html?autoconnect=true&resize=remote&path=websockify%3Ftoken%3D${FG_SERVICE_TOKEN}"
+      container: docker://ghcr.io/janeliascicomp/fg-interactive-apps/desktop:1.0.0
+      command: /opt/fg-desktop/start-desktop.sh
+      parameters:
+          - name: Data Folder
+            type: directory
+            description: >-
+                Optional folder to show on the desktop. Must be within a
+                mounted file share; it is bind-mounted into the container
+                automatically. Your home directory is always available.
+            required: false
+            exists: true
+
+      resources:
+          cpus: 4
+          memory: "16 GB"
+          walltime: "08:00"

desktop/start-desktop.sh

@@ -0,0 +1,126 @@
+#!/bin/bash
+# Fileglancer Remote Desktop launcher: an XFCE session on a VNC server, served
+# to the browser by noVNC/websockify on the single Fileglancer-provided port.
+#
+# Connection chain, and how each hop is protected on a shared compute node:
+#
+#   browser --HTTP/WS, ?token=$FG_SERVICE_TOKEN--> websockify 0.0.0.0:$FG_SERVICE_PORT
+#     --unix socket named after the token, in a 0700 dir--> Xvnc (TCP disabled)
+#       --X11 display, xauth cookie required--> XFCE session, Fiji, ...
+#
+# - websockify's UnixDomainSocketDirectory token plugin only tunnels WebSocket
+#   connections whose ?token= matches a socket filename in the private
+#   directory, so network access requires the per-job 192-bit token.
+# - Xvnc listens only on that unix socket (-rfbport -1 disables TCP). The 0700
+#   directory keeps other users on the node from reaching the VNC server at
+#   all, which is what makes -SecurityTypes None safe here.
+# - The X display itself requires the xauth cookie (mode 0600), so other local
+#   users cannot attach through /tmp/.X11-unix either.
+
+set -euo pipefail
+
+: "${FG_SERVICE_PORT:?FG_SERVICE_PORT is not set - this app requires the Fileglancer service contract}"
+: "${FG_SERVICE_TOKEN:?FG_SERVICE_TOKEN is not set - this app requires the Fileglancer service contract}"
+
+DATA_DIR="${1:-}"
+GEOMETRY="${FG_DESKTOP_GEOMETRY:-1920x1080}"
+
+# Private per-session state (X auth cookie, VNC socket, XDG runtime). This must
+# be on node-local disk - unix sockets are unreliable on NFS homes - and
+# mktemp -d creates it mode 0700, which is what keeps other users out.
+PRIV_DIR="$(mktemp -d /tmp/fg-desktop.XXXXXXXX)"
+SOCK_DIR="$PRIV_DIR/sock"
+XAUTH_FILE="$PRIV_DIR/Xauthority"
+VNC_SOCKET="$SOCK_DIR/$FG_SERVICE_TOKEN"
+export XDG_RUNTIME_DIR="$PRIV_DIR/run"
+mkdir -m 700 "$SOCK_DIR" "$XDG_RUNTIME_DIR"
+
+XVNC_PID=""
+SESSION_PID=""
+cleanup() {
+  if [ -n "$SESSION_PID" ]; then kill "$SESSION_PID" 2>/dev/null || true; fi
+  if [ -n "$XVNC_PID" ]; then kill "$XVNC_PID" 2>/dev/null || true; fi
+  rm -rf "$PRIV_DIR"
+}
+trap cleanup EXIT
+
+# --- Xvnc --------------------------------------------------------------------
+# Scan for a free X display (vncserver-style). Another user on the node can
+# grab a display between our check and Xvnc's startup, so on failure move on
+# to the next number.
+DISPLAY_NUM=""
+for n in $(seq 10 99); do
+  [ -e "/tmp/.X${n}-lock" ] && continue
+  [ -e "/tmp/.X11-unix/X${n}" ] && continue
+
+  # The cookie must exist before Xvnc starts: -auth is read at server startup.
+  rm -f "$XAUTH_FILE" && touch "$XAUTH_FILE" && chmod 600 "$XAUTH_FILE"
+  xauth -f "$XAUTH_FILE" add ":${n}" MIT-MAGIC-COOKIE-1 "$(mcookie)" 2>/dev/null
+
+  Xvnc ":${n}" \
+    -rfbunixpath "$VNC_SOCKET" -rfbunixmode 0600 \
+    -rfbport -1 \
+    -SecurityTypes None \
+    -auth "$XAUTH_FILE" \
+    -geometry "$GEOMETRY" -depth 24 \
+    -desktop "Fileglancer Desktop" &
+  XVNC_PID=$!
+
+  # Up when the VNC unix socket appears; dead (lost the display race) if Xvnc exits.
+  for _ in $(seq 1 50); do
+    [ -S "$VNC_SOCKET" ] && break
+    kill -0 "$XVNC_PID" 2>/dev/null || break
+    sleep 0.2
+  done
+  if [ -S "$VNC_SOCKET" ]; then
+    DISPLAY_NUM="$n"
+    break
+  fi
+  kill "$XVNC_PID" 2>/dev/null || true
+  wait "$XVNC_PID" 2>/dev/null || true
+  XVNC_PID=""
+  rm -f "$VNC_SOCKET"
+done
+
+if [ -z "$DISPLAY_NUM" ]; then
+  echo "ERROR: could not start Xvnc on any display (:10-:99)" >&2
+  exit 1
+fi
+
+export DISPLAY=":${DISPLAY_NUM}"
+export XAUTHORITY="$XAUTH_FILE"
+echo "Xvnc up on display ${DISPLAY} (unix socket only, no TCP)" >&2
+
+# --- Desktop conveniences ------------------------------------------------
+# $HOME is the user's real (bind-mounted) home, so these persist across sessions.
+mkdir -p "$HOME/Desktop"
+if [ ! -e "$HOME/Desktop/fiji.desktop" ]; then
+  cp /usr/share/applications/fiji.desktop "$HOME/Desktop/" 2>/dev/null || true
+  chmod +x "$HOME/Desktop/fiji.desktop" 2>/dev/null || true
+fi
+
+# Link the requested data folder onto the desktop (Fileglancer has already
+# bind-mounted it into the container).
+if [ -n "$DATA_DIR" ]; then
+  link_name="$HOME/Desktop/$(basename "$DATA_DIR")"
+  if [ ! -e "$link_name" ] || [ -L "$link_name" ]; then
+    ln -sfn "$DATA_DIR" "$link_name"
+  fi
+fi
+
+# --- XFCE session --------------------------------------------------------
+dbus-launch --exit-with-session startxfce4 &
+SESSION_PID=$!
+echo "XFCE session started (pid ${SESSION_PID})" >&2
+
+# --- websockify / noVNC ----------------------------------------------------
+# Serves the noVNC client and tunnels token-authenticated WebSocket
+# connections to the VNC unix socket. Runs in the foreground: stopping the
+# job (or websockify dying) tears down the whole session via the EXIT trap.
+echo "Serving noVNC on port ${FG_SERVICE_PORT}" >&2
+websockify \
+  --web /opt/novnc \
+  --token-plugin UnixDomainSocketDirectory \
+  --token-source "$SOCK_DIR" \
+  --heartbeat 30 \
+  "0.0.0.0:${FG_SERVICE_PORT}"