# 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
```