Add Xpra and IGV (v2.19.4) Java desktop example

shiny-simple-example/Dockerfile

@@ -58,4 +58,4 @@ ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]
 # 4) Command: Run your Shiny app via micromamba
 # ---------------------------------------------------------------
 # The port is set by CONNECT_TOOL_PORT environment variable
-CMD ["micromamba", "run", "-n", "shiny", "R", "-e", "shiny::runApp('/app/app_plot_demo.R', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"] 
+CMD ["micromamba", "run", "-n", "shiny", "R", "-e", "shiny::runApp('/app/app_plot_demo.R', host='0.0.0.0', port=as.integer(Sys.getenv('CONNECT_TOOL_PORT')))"] 

xpra-igv/Dockerfile

@@ -0,0 +1,115 @@
+# Add a default Connect client version. Can be overridden by build arg
+ARG CONNECT_CLIENT_VERSION="0.8.1-snapshot"
+
+# Path to the public connect-client
+FROM public.cr.seqera.io/platform/connect-client:${CONNECT_CLIENT_VERSION} AS connect
+
+FROM mambaorg/micromamba:1.5.10-noble AS micromamba
+
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG MAMBA_USER=root
+ARG MAMBA_USER_ID=0
+ARG MAMBA_USER_GID=0
+ENV MAMBA_USER=$MAMBA_USER
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+ENV MAMBA_EXE="/bin/micromamba"
+
+USER $MAMBA_USER
+
+RUN apt-get update --yes && apt-get install --yes --no-install-recommends \
+    apt-transport-https \
+    pciutils \
+    cups-filters \
+    cups-common \
+    cups-pdf \
+    ca-certificates \
+    git \
+    wget \
+    sudo \
+    libatomic1 \
+    python3.12 \
+    python3-cups \
+    python3-xdg \
+    python3-pyinotify \
+    python3-paramiko \
+    python3-netifaces \
+    python-is-python3 \
+    gnome-menus \
+    curl \
+    locales \
+    openjdk-17-jre \
+    gnupg \
+    kmod \
+    x11-xkb-utils \
+    dbus-x11 \
+    xvfb \
+    terminator \
+    thunar && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
+COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
+COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
+
+RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
+    /usr/local/bin/_dockerfile_setup_root_prefix.sh
+SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
+
+
+# Install Xpra
+RUN wget -O "/usr/share/keyrings/xpra.asc" https://xpra.org/xpra.asc && \
+    wget -O "/etc/apt/sources.list.d/xpra.sources"  https://raw.githubusercontent.com/Xpra-org/xpra/master/packaging/repos/noble/xpra.sources
+
+ARG xpra_version=6.2.0-r2-1
+RUN apt-get update --yes && apt-get install --yes --no-install-recommends \
+    xpra-html5 \
+    xpra=${xpra_version} \
+    xpra-client=${xpra_version} \
+    xpra-client-gtk3=${xpra_version} \
+    xpra-server=${xpra_version} \
+    xpra-codecs=${xpra_version} \
+    xpra-codecs-extras=${xpra_version} \
+    xpra-common=${xpra_version} \
+    xpra-x11=${xpra_version} && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
+    dpkg-reconfigure --frontend=noninteractive locales && \
+    update-locale LANG=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+# Create a conda env with the most recent compatible IGV
+RUN rm -rf /opt/conda/pkgs/*.lock && \
+    micromamba create -y -n igv -c bioconda \
+    igv \
+    && micromamba clean --all --yes \
+    && rm -rf /opt/conda/pkgs/*.lock
+
+# Copy the menu item contents, add to the env, make it executable
+COPY ./menu_items.txt /usr/share/applications/.desktop
+RUN chmod +x /usr/share/applications/.desktop
+
+# Copy the welcome message into the container and append it to the .bashrc
+COPY ./welcome_ASCII.txt /root/.welcome_ASCII.txt
+RUN echo "cat /root/.welcome_ASCII.txt" >> /root/.bashrc
+COPY ./entry.sh /bin
+
+COPY ./seqera-wallpaper.png /usr/share/xpra/www/background.png
+
+WORKDIR /workspace
+RUN ln -s /workspace /root
+
+# Add connect binary
+COPY --from=connect /usr/bin/connect-client /usr/bin/connect-client
+# Install connect dependencies
+RUN /usr/bin/connect-client --install
+# Optionally set tool identifier for metrics tracking purposes
+RUN /usr/bin/connect-client --setToolIdentifier custom
+
+ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]
+CMD ["bash",  "/bin/entry.sh"]

xpra-igv/README.md

@@ -0,0 +1,75 @@
+# Xpra and Integrative Genomics Viewer (IGV) Studio Environment
+
+This repository provides a custom container image for running
+[Xpra](https://xpra.org/index.html) and the [IGV](https://igv.org/)
+desktop Java application as a Studio environment in Seqera Platform.
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Features](#features)
+- [Prerequisites](#prerequisites)
+- [Building the Container](#building-the-container)
+- [Using in Seqera Studios](#using-in-seqera-studios)
+- [Customizing the Environment](#customizing-the-environment)
+- [References](#references)
+
+## Overview
+
+This container is designed for use as a [custom Studio
+environment](https://docs.seqera.io/platform-cloud/studios/custom-envs) in
+Seqera Platform. It is based on the required Seqera base image and
+includes the necessary `connect-client` for compatibility.
+
+## Features
+
+- Open-source, remote desktop display server
+- IGV desktop Java application (v2.19.4)
+- Reproducible and git-friendly
+- Compatible with Seqera Studios custom environments
+
+## Prerequisites
+
+- [Docker](https://www.docker.com/) installed
+- [Wave](https://docs.seqera.io/platform-cloud/wave/) configured
+in your Seqera Platform workspace (required for custom environments)
+- Access to a container registry (public or Amazon ECR) if you wish to push your image
+
+## Building the Container
+
+To build the container locally:
+
+```sh
+wave -f Dockerfile --await
+```
+
+Or, using Docker directly:
+
+```sh
+docker build -t xpra-igv .
+```
+
+## Using in Seqera Studios
+
+1. **Push your image** to a container registry accessible by Seqera Platform.
+2. In Seqera Platform, go to the **Studios** tab and click **Add Studio**.
+3. Select **Prebuilt container image** as the template.
+4. Enter your container image URI (e.g., `cr.your-registry.io/your-org/marimo-studio:latest`).
+5. Configure compute resources and data mounts as needed.
+6. Launch the Studio.
+
+For more details, see the [official documentation](https://docs.seqera.io/platform-cloud/studios/custom-envs).
+
+## Customizing the Environment
+
+You can further customize this environment by:
+
+- Adding Conda or pip packages (see [Conda package syntax](https://docs.seqera.io/platform-cloud/studios/custom-envs#conda-package-syntax))
+- Modifying the Dockerfile to include additional dependencies
+
+## References
+
+- [Seqera Studios: Custom Environments](https://docs.seqera.io/platform-cloud/studios/custom-envs)
+- [Xpra Documentation](https://github.com/Xpra-org/xpra/blob/master/README.md)
+- [IGV Desktop Documentation](https://github.com/igvteam/igv)
+- [Wave Documentation](https://docs.seqera.io/platform-cloud/wave/)

xpra-igv/entry.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+source /usr/local/bin/_activate_current_env.sh
+# automatically initialize all future (bash) shells, so that micromambe environments can be activated and deactivated
+micromamba shell init --shell bash --root-prefix=~/micromamba
+
+# Default video encoder
+video_encoder="x264"
+
+# Check for NVIDIA or AMD GPU presence
+if lspci | grep -E "VGA|3D|NVIDIA|AMD"; then
+    # Assuming the presence of NVIDIA drivers and utilities
+    if command -v nvidia-smi &> /dev/null; then
+        video_encoder="nvenc"
+    elif glxinfo | grep -i "direct rendering: Yes"; then
+        # Check for AMD or other GPU types that support VA-API (Intel included)
+        video_encoder="vaapi"
+    fi
+fi
+
+exec xpra start \
+--bind-tcp=0.0.0.0:$CONNECT_TOOL_PORT \
+--mdns=no \
+--html=on \
+--pulseaudio=no \
+--clipboard-direction=both \
+--clipboard=yes \
+--dpi=300 \
+--encoding=auto \
+--video-encoder=$video_encoder \
+--min-quality=95 \
+--min-speed=95 \
+--desktop-scaling=auto \
+--windows=yes \
+--daemon=no \
+--start-child="terminator" \
+--start-child="igv" \
+--idle-timeout=21600 \
+--mousewheel=on \
+--opengl=yes \
+--tray=yes \
+--system-tray=yes \
+--sharing=yes \
+--ssl=www \
+--exit-with-client=no \
+--file-transfer=on \
+--open-files=no \
+--webcam=no \
+--notifications=no \
+--bell=no :100

xpra-igv/menu_items.txt

@@ -0,0 +1,9 @@
+[Desktop Entry]
+Version=1.0
+Type=Application
+Name=IGV
+Comment=Integrative Genomics Viewer
+Exec=/opt/conda/bin/igv
+Icon=utilities-terminal
+Terminal=false
+Categories=System;Science;Biology;

xpra-igv/welcome_ASCII.txt

@@ -0,0 +1,15 @@
+.--------------------------------------------------------------------------.
+|                                                                          |
+|   ____                              ____  _             _ _              |
+|  / ___|  ___  __ _  ___ _ __ __ _  / ___|| |_ _   _  __| (_) ___  ___    |
+|  \___ \ / _ \/ _` |/ _ \ '__/ _` | \___ \| __| | | |/ _` | |/ _ \/ __|   |
+|   ___) |  __/ (_| |  __/ | | (_| |  ___) | |_| |_| | (_| | | (_) \__ \   |
+|  |____/ \___|\__, |\___|_|  \__,_| |____/ \__|\__,_|\__,_|_|\___/|___/   |
+|  __  __         |_|              ___ ______     __                       |
+|  \ \/ /_ __  _ __ __ _     _    |_ _/ ___\ \   / /                       |
+|   \  /| '_ \| '__/ _` |  _| |_   | | |  _ \ \ / /                        |
+|   /  \| |_) | | | (_| | |_   _|  | | |_| | \ V /                         |
+|  /_/\_\ .__/|_|  \__,_|   |_|   |___\____|  \_/                          |
+|       |_|                                                                |
+|                                                                          |
+'--------------------------------------------------------------------------'