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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.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

      3.4. 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.

      4.5. 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.

      5.6. 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.

      6.7. 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.

                7.8. 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

                IfCheck Maven is missing:installation:

                mvn --version

                If the command is not found, contact Ruman.

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