qupath_plus.def

Bootstrap: docker
From: amd64/ubuntu:jammy

%post
# install needed dependencies
    rm -rf /var/lib/apt/lists/*
    apt-get update -y
    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         ca-certificates \
         wget \
         netcat \
         libgl1 \
         xz-utils \
         openjfx \
         unzip \
         curl \
         xterm \
         uuid-runtime

# Install latest Xpra and dependencies
    apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y wget gnupg2 apt-transport-https \
    software-properties-common ca-certificates && \
    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/jammy/xpra.sources

    apt-get update && \
    DEBIAN_FRONTEND=noninteractive apt-get install -yqq \
    xpra \
    xvfb \
    xterm \
    sshfs && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*


# Install latest QuPath release from GitHub
    LATEST_VERSION=$(curl --silent -I https://github.com/qupath/qupath/releases/latest/ | grep location | awk -F/ '{print $NF'} | tr -d '\r')
    wget https://github.com/qupath/qupath/releases/download/$LATEST_VERSION/QuPath-${LATEST_VERSION}-Linux.tar.xz
    tar xvf QuPath-${LATEST_VERSION}-Linux.tar.xz
    mv QuPath-${LATEST_VERSION}-Linux/QuPath .
    rm QuPath-${LATEST_VERSION}-Linux.tar.xz
    rm -r QuPath-${LATEST_VERSION}-Linux
# set permissions to make it executable
    chmod a+x QuPath/bin/QuPath

# install extensions for 0.5.x
    cd QuPath/lib/app/
    wget https://github.com/qupath/qupath-extension-djl/releases/download/v0.3.0/qupath-extension-djl-0.3.0.jar
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/qupath-extension-djl-0.3.0.jar' QuPath.cfg

    wget https://github.com/qupath/qupath-extension-stardist/releases/download/v0.5.0/qupath-extension-stardist-0.5.0.jar
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/qupath-extension-stardist-0.5.0.jar' QuPath.cfg

    wget https://github.com/qupath/qupath-extension-bioimageio/releases/download/v0.1.0/qupath-extension-bioimageio-0.1.0.jar
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/qupath-extension-bioimageio-0.1.0.jar' QuPath.cfg

    wget https://github.com/BIOP/qupath-extension-biop-omero/releases/download/v1.0.3/qupath-extension-biop-omero-1.0.3.zip
    unzip qupath-extension-biop-omero-1.0.3.zip
    rm qupath-extension-biop-omero-1.0.3.zip
    
    wget https://github.com/ome/openmicroscopy/releases/download/v5.6.13/OMERO.java-5.6.13-ice36.zip
    unzip OMERO.java-5.6.13-ice36.zip
    mv OMERO.java-5.6.13-ice36/libs .
    rm OMERO.java-5.6.13-ice36.zip
    rm -d OMERO.java-5.6.13-ice36
    
    # update classpaths so the omero extension uses the app path
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/qupath-extension-biop-omero-1.0.3.jar' QuPath.cfg
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/simple-omero-client-5.18.0.jar' QuPath.cfg
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/libs/*' QuPath.cfg

    wget https://github.com/qupath/qupath-extension-omero-web/releases/download/v0.4.0/qupath-extension-omero-0.4.0.jar
    sed -i '/^\[Application\]$/a app.classpath=$APPDIR/qupath-extension-omero-0.4.0.jar' QuPath.cfg

%runscript
    #!/bin/bash
    mkdir -p $HOME/.xpra
    chmod 700 $HOME/.xpra
    export XDG_RUNTIME_DIR=$HOME/.xpra
    export DISPLAY=:$(shuf -n 1 -i 100-200)
    while PORT=$(shuf -n 1 -i 49152-65535); nc -z 0.0.0.0 $PORT; do continue; done
    export XPRA_PASSWORD=$(uuidgen)
    echo "========================================="
    echo "Password is $XPRA_PASSWORD"
    echo "Launching QuPath to display via Xpra on DISPLAY $DISPLAY. Connect via"
    echo "http://$(hostname -i):$PORT/?password=$XPRA_PASSWORD"
    echo "Logging errors to /tmp/xpra.log"
    echo "========================================="
    xpra start \
    --minimal=yes \
    --bind-tcp=0.0.0.0:$PORT,auth=env \
    --websocket-upgrade=yes \
    --socket-dirs=$XDG_RUNTIME_DIR \
    --opengl=yes \
    --html=on \
    --compression-level=1 \
    --start="/QuPath/bin/QuPath" \
    --exit-with-windows=yes \
    --daemon=no \
    --clipboard=yes \
    --xvfb="/usr/bin/Xvfb +extension Composite -screen 0 1920x1080x24+32 -nolisten tcp -noreset -auth $XAUTHORITY" \
    $DISPLAY \
    2>/tmp/xpra.log | tee --append /tmp/xpra.log