# 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
```
---
# 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
```