Skip to main content

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

  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
Back to top