Runing JIPipe on server Prepackaged Running JIPipe on a Linux Server using MobaXterm This guide explains how to upload and run the prepackaged Linux version of JIPipe on a remote server using MobaXterm on Windows. 1. Download JIPipe Open the official JIPipe download page: https://jipipe.hki-jena.de/download Download the Prepackaged Linux64 ZIP package. The prepackaged version already contains Fiji/ImageJ and JIPipe. Linux instructions are also available here: https://applied-systems-biology.github.io/JIPipe-Documentation/prepackaged-jipipe.html#-uj2awg_7 2. Connect to the Server using MobaXterm Open MobaXterm Click Session Select SSH Enter: Remote host : your server hostname or IP Specify username : your Linux username Click OK You will now get a Linux terminal inside MobaXterm. 3. Upload the ZIP File MobaXterm includes a built-in SFTP file browser on the left side. Method 1: Drag and Drop (Recommended) Drag the downloaded JIPipe-*-Prepackaged-Linux64.zip file into the desired server directory. Example destination: /opt/jipipe/ Method 2: Use SCP Command You can also upload from the terminal: scp JIPipe-*-Prepackaged-Linux64.zip username@server:/opt/jipipe/ 4. Unpack the ZIP File Inside the terminal: cd /opt/jipipe unzip JIPipe-5.3.0-Prepackaged-Linux64.zip This creates the extracted JIPipe directory. 5. Fix Permissions (Important) If you get a Permission denied error when starting JIPipe, make the launcher executable. The launcher scripts are located inside the bin folder: cd JIPipe/bin chmod +x ImageJ-linux64 chmod +x jipipe.sh You can verify the permissions: ls -l ImageJ-linux64 ls -l jipipe.sh 6. Start JIPipe Start JIPipe using: bash jipipe.sh or: ./jipipe.sh 7. Running JIPipe on Remote Servers For remote Linux servers, we currently recommend using MobaXterm X11 forwarding to display the JIPipe GUI remotely. MobaXterm automatically provides an X11 server on Windows. Before connecting: Open MobaXterm Go to: Settings → X11 Ensure: X11 server is enabled When creating the SSH session: Open Session Select SSH Enable: X11-Forwarding Then connect normally and start JIPipe: cd /opt/jipipe/JIPipe/bin bash jipipe.sh The JIPipe GUI should appear on your Windows desktop. 8. Advanced / Untested: Headless Execution using Xvfb ⚠️ Advanced / currently untested setup. If the server has no graphical desktop environment, it may be possible to run JIPipe using a virtual display with Xvfb . Install: sudo apt install xvfb Run: xvfb-run bash jipipe.sh This setup has not been fully tested with JIPipe workflows. 9. Keep JIPipe Running after Disconnecting Use screen : screen -S jipipe cd /opt/jipipe/JIPipe/bin bash jipipe.sh Detach from the session: Ctrl+A then D Reconnect later: screen -r jipipe Building on the server Building JIPipe from Source on a Linux Server using MobaXterm This guide explains how to build and run JIPipe from source code on a Linux server using MobaXterm and IntelliJ Remote Development . 1. Requirements JIPipe requires: Java Maven Git Maven is already installed on the Chrysos server at the moment. If Maven or Java is missing on another server, contact Ruman for installation support. All steps below are performed through MobaXterm . 2. Connect to the Server using MobaXterm Open MobaXterm Click Session Select SSH Enter: Remote host : your server hostname or IP Specify username : your Linux username Click OK You should now have a Linux terminal inside MobaXterm. 3. Clone the JIPipe Repository Clone the repository from the internal ASB GitLab server: git clone https://asb-git.hki-jena.de/RGerst/jipipe Go into the repository: cd jipipe You can either: build directly on master or switch to your own branch Example: git checkout my-branch 4. Recommended: Use IntelliJ Remote Development We strongly recommend using IntelliJ IDEA Remote Development for building JIPipe on remote servers. Benefits: easier Maven handling easier indexing integrated terminal easier debugging easier remote GUI support Open the remote project in IntelliJ and allow Maven indexing to finish before building. 5. Install Missing Maven Dependencies (Very Important) Some Maven dependencies are no longer available online and must be copied manually. Download or copy the dependency files from: https://asb-git.hki-jena.de/RGerst/jipipe-distribution-files/-/tree/main/scripts/maven-dependencies?ref_type=heads These dependencies must be copied into the local Maven repository: ~/.m2/repository The .m2 folder is hidden. To locate it: cd ~ ls -A You should see: .m2 Copy the dependency folders into: ~/.m2/repository ⚠️ This step is extremely important. Without these dependencies the Maven build may fail. You can use the MobaXterm file browser (left side panel) to drag-and-drop the dependency folders into the correct location. 6. Build JIPipe Inside the repository root: cd ~/jipipe Run a full Maven install: mvn clean install This may take a long time during the first build. Wait until all JAR files are built successfully. 7. Run JIPipe from Source After the build finishes, start JIPipe using: java --add-opens=java.base/java.lang=ALL-UNNAMED -cp "$(cat jipipe-launcher/cp.txt):jipipe-launcher/target/classes" org.hkijena.jipipe.launcher.JIPipeLauncher Example terminal location: (base) dkhatri@chrysos:~/jipipe$ If everything was built correctly, JIPipe should start normally. For remote GUI usage, we recommend using MobaXterm X11 forwarding . Before connecting: Open MobaXterm Go to: Settings → X11 Ensure: X11 server is enabled When creating the SSH session: Open Session Select SSH Enable: X11-Forwarding Then launch JIPipe normally. The JIPipe GUI should appear on your Windows desktop. 8. Troubleshooting Missing Dependencies If Maven reports missing artifacts: verify that all manually provided dependencies were copied into: ~/.m2/repository restart IntelliJ Maven indexing if necessary Permission Issues If scripts cannot be executed: chmod +x *.sh Maven Not Found Check Maven installation: mvn --version If the command is not found, contact Ruman .