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 .