# 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](https://jipipe.hki-jena.de/download?utm_source=chatgpt.com) 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](https://applied-systems-biology.github.io/JIPipe-Documentation/prepackaged-jipipe.html#-uj2awg_7) --- # 2. Connect to the Server using MobaXterm 1. Open **MobaXterm** 2. Click **Session** 3. Select **SSH** 4. Enter: - **Remote host**: your server hostname or IP - **Specify username**: your Linux username 5. 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: 1. Open **MobaXterm** 2. Go to: - **Settings → X11** 3. Ensure: - **X11 server is enabled** When creating the SSH session: 1. Open **Session** 2. Select **SSH** 3. 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 1. Open **MobaXterm** 2. Click **Session** 3. Select **SSH** 4. Enter: - **Remote host**: your server hostname or IP - **Specify username**: your Linux username 5. 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](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: 1. Open **MobaXterm** 2. Go to: - **Settings → X11** 3. Ensure: - **X11 server is enabled** When creating the SSH session: 1. Open **Session** 2. Select **SSH** 3. 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**.