Merge pull request #36 from seqeralabs/cursor/kasmvnc-qupath-f4f3

Add KasmVNC QuPath studio branch

Author: FloWuenne

.github/workflows/docker-pr.yml

@@ -15,52 +15,22 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
       - name: Detect changed Dockerfiles
         id: changes
-        uses: dorny/paths-filter@v3
+        uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36
         with:
           filters: |
-            ttyd:
-              - 'ttyd/**'
-            streamlit:
-              - 'streamlit/**'
-            cellxgene:
-              - 'cellxgene/**'
-            shiny:
-              - 'shiny-simple-example/**'
-            marimo:
-              - 'marimo/**'
-            napari:
-              - 'kasmVNC/napari/**'
-            qupath:
-              - 'kasmVNC/qupath/**'
+            kasmvnc_qupath:
+              - '.seqera/**'
 
       - name: Set matrix
         id: set-matrix
         run: |
           CONTAINERS="[]"
-          if [[ "${{ steps.changes.outputs.ttyd }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"ttyd","path":"./ttyd"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.streamlit }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"streamlit","path":"./streamlit"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.cellxgene }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"cellxgene","path":"./cellxgene"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.shiny }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"shiny","path":"./shiny-simple-example"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.marimo }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"marimo","path":"./marimo"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.napari }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"napari","path":"./kasmVNC/napari"}]')
-          fi
-          if [[ "${{ steps.changes.outputs.qupath }}" == "true" ]]; then
-            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"qupath","path":"./kasmVNC/qupath"}]')
+          if [[ "${{ steps.changes.outputs.kasmvnc_qupath }}" == "true" ]]; then
+            CONTAINERS=$(echo "$CONTAINERS" | jq -c '. + [{"name":"kasmvnc-qupath","path":"./.seqera"}]')
           fi
           echo "matrix={\"container\":$CONTAINERS}" >> "$GITHUB_OUTPUT"
 
@@ -79,44 +49,44 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v3
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GHCR_TOKEN }}
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2
 
       - name: Extract metadata
         id: meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
         with:
           images: ${{ env.REGISTRY }}/${{ github.repository }}/development
           tags: |
             type=ref,event=pr,prefix=${{ matrix.container.name }}-pr
 
       - name: Build and push ${{ matrix.container.name }}
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25
         with:
           context: ${{ matrix.container.path }}
           push: true
           platforms: linux/amd64
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha,scope=${{ matrix.container.name }}
-          cache-to: type=gha,mode=max,scope=${{ matrix.container.name }}
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository }}/development:${{ matrix.container.name }}-buildcache
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository }}/development:${{ matrix.container.name }}-buildcache,mode=max
 
       - name: Get image reference for scan
         id: scanref
         run: |
           echo "ref=${{ fromJSON(steps.meta.outputs.json).tags[0] }}" >> $GITHUB_OUTPUT
 
       - name: Run security scan
-        uses: aquasecurity/trivy-action@0.31.0
+        uses: aquasecurity/trivy-action@76071ef0d7ec797419534a183b498b4d6366cf37
         with:
           image-ref: ${{ steps.scanref.outputs.ref }}
           format: "table"
@@ -137,7 +107,7 @@ jobs:
           fi
 
       - name: Upload security scan results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02
         if: always()
         with:
           name: trivy-scan-${{ matrix.container.name }}-${{ github.run_id }}
@@ -155,7 +125,7 @@ jobs:
           echo "- **Commit**: \`${{ github.sha }}\`" >> $GITHUB_STEP_SUMMARY
 
       - name: Comment on PR
-        uses: actions/github-script@v7
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea
         with:
           script: |
             const fs = require('fs');

.github/workflows/docker-release.yml

@@ -8,13 +8,7 @@ on:
         required: true
         type: choice
         options:
-          - ttyd
-          - streamlit
-          - cellxgene
-          - shiny
-          - marimo
-          - napari
-          - qupath
+          - kasmvnc-qupath
       version:
         description: 'Version to release (e.g., 1.0.0)'
         required: true
@@ -38,34 +32,28 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
       - name: Set container path
         id: container
         run: |
           case "${{ inputs.container }}" in
-            ttyd) echo "path=./ttyd" >> "$GITHUB_OUTPUT" ;;
-            streamlit) echo "path=./streamlit" >> "$GITHUB_OUTPUT" ;;
-            cellxgene) echo "path=./cellxgene" >> "$GITHUB_OUTPUT" ;;
-            shiny) echo "path=./shiny-simple-example" >> "$GITHUB_OUTPUT" ;;
-            marimo) echo "path=./marimo" >> "$GITHUB_OUTPUT" ;;
-            napari) echo "path=./kasmVNC/napari" >> "$GITHUB_OUTPUT" ;;
-            qupath) echo "path=./kasmVNC/qupath" >> "$GITHUB_OUTPUT" ;;
+            kasmvnc-qupath) echo "path=./.seqera" >> "$GITHUB_OUTPUT" ;;
           esac
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v3
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GHCR_TOKEN }}
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2
 
       - name: Extract metadata
         id: meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
         with:
           images: ${{ env.REGISTRY }}/${{ github.repository }}/${{ inputs.container }}
           tags: |
@@ -76,7 +64,7 @@ jobs:
             org.opencontainers.image.licenses=MIT
 
       - name: Build and push ${{ inputs.container }}
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25
         with:
           context: ${{ steps.container.outputs.path }}
           push: true
@@ -85,11 +73,11 @@ jobs:
             CONNECT_CLIENT_VERSION=${{ inputs.connect_client_version || '0.9' }}
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha,scope=${{ inputs.container }}
-          cache-to: type=gha,mode=max,scope=${{ inputs.container }}
+          cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository }}/${{ inputs.container }}:buildcache
+          cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository }}/${{ inputs.container }}:buildcache,mode=max
 
       - name: Create GitHub Release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@72f2c25fcb47643c292f7107632f7a47c1df5cd8
         with:
           tag_name: ${{ inputs.container }}/${{ inputs.version }}
           name: ${{ inputs.container }} ${{ inputs.version }}

kasmVNC/qupath/Dockerfile .seqera/DockerfilekasmVNC/qupath/Dockerfile renamed to .seqera/Dockerfile

@@ -14,14 +14,16 @@ LABEL org.opencontainers.image.source="https://github.com/seqeralabs/custom-stud
 
 ENV TITLE="QuPath"
 
-# KasmVNC Performance Optimizations
+# KasmVNC performance tuning for interactive desktop streaming
 ENV KASM_VNC_ENABLE_WEBP=1
 ENV KASM_VNC_JPEG_QUALITY=5
 ENV KASM_VNC_MAX_FRAME_RATE=30
 ENV KASM_VNC_THREADS=4
 
-# Install dependencies for QuPath
-RUN apt-get update && apt-get install -y --no-install-recommends \
+# Install dependencies for QuPath. The base image can carry stale third-party apt
+# sources, so drop NodeSource before refreshing Ubuntu package indexes.
+RUN rm -f /etc/apt/sources.list.d/nodesource*.list \
+    && apt-get update && apt-get install -y --no-install-recommends \
     wget \
     xz-utils \
     libgl1 \
@@ -39,6 +41,10 @@ RUN wget -q https://github.com/qupath/qupath/releases/download/v${QUPATH_VERSION
     && chmod +x /opt/qupath/bin/QuPath \
     && rm /tmp/qupath.tar.xz
 
+
+# Create the X socket directory before KasmVNC drops privileges to the abc user.
+RUN sed -i '/^exec s6-setuidgid/i mkdir -p /tmp/.X11-unix && chmod 1777 /tmp/.X11-unix' /etc/s6-overlay/s6-rc.d/svc-kasmvnc/run
+
 # Single-app mode: application launches directly, no desktop
 RUN echo "/opt/qupath/bin/QuPath" > /defaults/autostart
 
@@ -56,8 +62,8 @@ COPY --from=connect /usr/bin/connect-client /usr/bin/connect-client
 # Install connect-client
 RUN /usr/bin/connect-client --install
 
-# Seqera Studios entrypoint (connect-client handles fusion filesystem)
+# Seqera Studios entrypoint (connect-client handles Fusion filesystem)
 ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]
 
-# CMD bridges CONNECT_TOOL_PORT to KasmVNC's CUSTOM_PORT and launches the init
+# Bridge CONNECT_TOOL_PORT to KasmVNC's CUSTOM_PORT and launch the init system
 CMD ["/bin/bash", "-c", "export CUSTOM_PORT=${CONNECT_TOOL_PORT:-6901} && exec /init"]

.seqera/studio-config.yaml

@@ -0,0 +1,6 @@
+schemaVersion: "0.0.1"
+kind: "studio-config"
+session:
+  template:
+    kind: "dockerfile"
+    dockerfile: "Dockerfile"

README.md

@@ -1,92 +1,70 @@
-# Custom Studios Examples
+# QuPath KasmVNC Studio Environment
 
-This repository contains example Dockerfiles and configurations for custom Seqera Studio applications. Each example demonstrates how to create and deploy different types of interactive applications in Seqera Studios.
+This branch contains the Seqera Studios configuration for running [QuPath](https://qupath.github.io/) with [KasmVNC](https://kasmweb.com/kasmvnc), making the QuPath desktop available through a browser in Seqera Platform.
 
-## Available Examples
+> This is a branch of the [custom-studios-examples](https://github.com/seqeralabs/custom-studios-examples) repository. Each branch contains a different custom Studio configuration. See the `master` branch for an overview of all available Studios.
 
-- [Marimo](marimo/README.md) - A reactive Python notebook environment
-- [CellxGene](cellxgene/README.md) - Interactive single-cell data visualization
-- [Streamlit](streamlit/README.md) - MultiQC visualization using Streamlit
-- [Shiny](shiny-simple-example/README.md) - Interactive data visualization with R Shiny
-- [TTYD](ttyd/README.md) - Interactive web-based terminal with bioinformatics tools
+## Quick Start
 
-## Prerequisites
+### Add from Git Repository
 
-All examples in this repository require:
-- [Docker](https://www.docker.com/) installed
-- [Wave](https://docs.seqera.io/platform-cloud/wave/) configured in your Seqera Platform workspace
-- Access to a container registry (public or Amazon ECR) for pushing your images
+1. Navigate to **Studios** > **Add Studio** in your Seqera Platform workspace
+2. Select **Git repository** as the source
+3. Enter the repository URL: `https://github.com/seqeralabs/custom-studios-examples`
+4. Select branch: `kasmvnc-qupath`
+5. Select your compute environment
+6. Click **Add** then **Start**
 
-## Common Features
+### Alternative: Use Pre-built Image
 
-All examples in this repository:
-- Are compatible with both local Docker testing and Seqera Studios
-- Use the required Seqera base image and connect-client
-- Include detailed setup and usage instructions
-- Support data mounting via datalinks in Studios
-- Are built for linux/amd64 platform compatibility
-- Use multi-stage builds to include the connect-client
-- Follow consistent container best practices
+```
+ghcr.io/seqeralabs/custom-studios-examples/kasmvnc-qupath:latest
+```
 
-## Deploying to Seqera Studios
+### Alternative: Build with Wave CLI
 
-All examples follow the same deployment process:
+```bash
+wave -f .seqera/Dockerfile --context .seqera --platform linux/amd64 --await --tower-token "$TOWER_ACCESS_TOKEN"
+```
 
-1. Select the **Studios** tab in your workspace
-2. Click **Add Studio**
-3. In the **General config** section:
-   - Select **Prebuilt container image** as the container template
-   - Enter your container image URI (e.g., `cr.seqera.io/scidev/your-example`)
-   - Set a **Studio name** and optional **Description**
-4. Configure compute resources in the **Compute and Data** section:
-   - Select your compute environment
-   - Adjust CPU, GPU, and memory allocations as needed
-   - Mount any required data using the **Mount data** option
-   - Configure environment variables if the example supports them (see [Environment Variables](#environment-variables) section)
-5. Review the configuration in the **Summary** section
-6. Click **Add and start** to create and launch the Studio
+## Features
 
-## Environment Variables
+- QuPath 0.6.0 bioimage analysis desktop
+- Browser access through LinuxServer.io KasmVNC
+- Single-app mode that launches QuPath directly
+- KasmVNC WebP, quality, frame-rate, and thread tuning for interactive use
+- Compatible with Seqera Studios custom environments and Data Link mounts
 
-Some examples support environment variable configuration to customize data paths and application settings without modifying the container image. This makes those examples more flexible and reusable across different datasets and configurations.
+> **Note:** QuPath is x86_64 only. Build and run this Studio as `linux/amd64`.
 
-### Examples with Environment Variables
+## Docker Image
 
-Only the following examples support environment variable configuration:
-- **CellxGene**: `DATASET_FILE`, `DATASET_TITLE` - Configure dataset path and display title
-- **Shiny**: `DATA_PATH` - Configure data file path with automatic cloud storage path conversion
+The container image is available at:
 
-### Examples without Environment Variables
+```
+ghcr.io/seqeralabs/custom-studios-examples/kasmvnc-qupath:latest
+```
 
-These examples work with their default configurations and don't require environment variable setup:
-- **Marimo**: Interactive Python notebook environment
-- **Streamlit**: MultiQC visualization with web-based data loading interface
-- **TTYD**: Web-based terminal with pre-installed bioinformatics tools
+## Local Testing
 
-### Using Environment Variables in Seqera Studios
+```bash
+cd .seqera
+docker build --platform=linux/amd64 --build-arg CONNECT_CLIENT_VERSION=0.9 -t kasmvnc-qupath .
+docker run --rm --platform linux/amd64 --shm-size=2g -p 6901:6901 --entrypoint /init kasmvnc-qupath
+```
 
-When deploying to Seqera Studios, you can configure environment variables in the **Compute and Data** section:
-1. Expand the **Environment variables** section
-2. Add key-value pairs for the variables you want to customize
-3. The application will use these values instead of the defaults
+QuPath will be available at http://localhost:6901.
 
-## Documentation
+## Configuration
 
-- [Official documentation on building custom studio environments](https://docs.seqera.io/platform-cloud/studios/custom-envs#custom-containers)
-- Each example's README contains specific instructions for:
-  - Building and testing locally
-  - Required dependencies and configurations
-  - Example-specific features and usage
-  - Data format requirements
-  - Customization options
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `CONNECT_TOOL_PORT` | Set by platform | KasmVNC web port in Seqera Studios |
+| `CUSTOM_PORT` | `CONNECT_TOOL_PORT` or `6901` | KasmVNC web port used by the base image |
 
-## Contributing
+## References
 
-Feel free to contribute new examples or improvements to existing ones. Each example should:
-- Follow the established README structure
-- Include comprehensive documentation
-- Maintain consistency with common features
-- Provide clear prerequisites and deployment instructions
-- Include example data or clear data requirements
-
-<!-- TODO Add a link to the blog post -->
+- [Seqera Studios: Custom Environments](https://docs.seqera.io/platform-cloud/studios/custom-envs)
+- [Seqera Studios: Add from Git Repository](https://docs.seqera.io/platform-cloud/studios/add-studio-git-repo)
+- [QuPath Documentation](https://qupath.readthedocs.io/)
+- [KasmVNC Documentation](https://kasmweb.com/kasmvnc)