### Build FragPipe Installer for Windows

Source: https://github.com/nesvilab/fragpipe/blob/develop/README.md

Use this command to build the Windows installer for FragPipe from the root directory of the repository. Ensure you are in the FragPipe-GUI directory before running.

```bash
cd FragPipe-GUI
./gradlew makeReleaseInstaller
```

--------------------------------

### Install Python Libraries with Pip

Source: https://github.com/nesvilab/fragpipe/wiki/Python

Use pip to install the necessary Python libraries for FragPipe. Ensure Python 3 is installed.

```bash
pip install numpy
pip install panda
pip install Cython
pip install msproteomicstools
```

--------------------------------

### Build FragPipe Zip for Linux

Source: https://github.com/nesvilab/fragpipe/blob/develop/README.md

Use this command to build the Linux zip archive for FragPipe from the root directory of the repository. Ensure you are in the FragPipe-GUI directory before running.

```bash
cd FragPipe-GUI
./gradlew makeReleaseZipLinux
```

--------------------------------

### Use Configuration File with DIA-NN

Source: https://github.com/nesvilab/fragpipe/blob/develop/tools/diann/1.8.2_beta_8/windows/README.md

Reference a configuration file containing DIA-NN commands using the --cfg option. This is useful for handling large experiments or custom pipelines.

```bash
--cfg diann_config.cfg
```