Installation

CoMPaseD is written in Python 3 and has been tested on Windows (≥ Windows 10) and Linux machines. Installation and program start should be done via the command prompt, while configuring and running CoMPaseD analyses is possible via the command prompt or the graphical interface.

Dependencies

Crux Toolkit

Binaries for the crux mass spectrometry analysis toolkit are available via the official crux webpage. Download the binaries suitable for your operating system (Windows/Linux) (version ≥ 3.2).

Python

To run CoMPaseD python (versions 3.5–3.12 tested) is required.

Note

While newer python versions may be compatible, some dependencies may not be immediately available for the latest releases. It is recommended to use a tested version to ensure full functionality.

Install python using:

Download Python for your Windows distribution.
Install Python by executing the downloaded file and following the instructions.

Python packages

The Python packages with suitable version numbers are listed in the provided requirements.txt.

requirements.txt

Package name	Version
bio	≥1.5.9
biopython	≥1.81
colorama	≥0.4
keras	≥2.13.1
matplotlib	=3.7.2
numpy	≥1.22
pandas	≥2.0
PyQt6-Qt6	≥6.5
PyQt6-sip	≥13.5
PyQt6	≥6.5
python-dateutil
tensorflow-estimator
tensorflow-intel
tensorflow-io-gcs-filesystem
tensorflow	≥2.12.0

Tip

We recommend using a virtual environment and pip to install these dependencies.

Install the Python requirements using pip and requirements.txt:

Set Installation Directory

Open a command-line window and navigate to the directory where you want to install CoMPaseD:
```
mkdir C:\Programs\CoMPaseD
cd C:\Programs\CoMPaseD
```
Clone the Repository

Copy the CoMPaseD repository into the chosen directory:
```
git clone https://github.com/MicrobialProteomics/CoMPaseD.git
```
Tip

The Git command may not be available by default in many Windows installations. You may need to install Git in advance.
Create and Activate a Virtual Environment

Set up a virtual environment to manage dependencies:
```
C:\Programs\python\python.exe -m venv venv
C:\Programs\CoMPaseD\venv\Scripts\activate.bat
```
Install Dependencies

Install the required Python packages:
```
python -m pip install -r requirements.txt
```
Run CoMPaseD

Launch the graphical interface:
```
CoMPaseD_gui.py
```
Configure Crux Path

Set the path to the Crux toolkit within the GUI and save the configuration. CoMPaseD is now ready to use.

Set Installation Directory

Open a command-line window and navigate to the directory where you want to install CoMPaseD:
```
mkdir -p  ~/Programs/CoMPaseD
cd ~/Programs/CoMPaseD
```
Clone the Repository

Copy the CoMPaseD repository into the chosen directory:
```
git clone https://github.com/MicrobialProteomics/CoMPaseD.git
```
Tip

If you do not have git installed. Install it using sudo apt install git or your prefered package manager.
Create and Activate a Virtual Environment

Set up a virtual environment to manage dependencies:
```
python -m venv venv
source venv/bin/activate
```
Install Dependencies

Install the required Python packages:
```
python -m pip install -r requirements.txt
```
Run CoMPaseD

Launch the graphical interface:
```
CoMPaseD_gui.py
```
Configure Crux Path

Set the path to the Crux toolkit within the GUI and save the configuration. CoMPaseD is now ready to use.

../_images/configuration-tab.png — Configuration tab upon first start of CoMPaseD. The red error message will disapear when the path to the crux executable is properly set and the configuration is saved.

You can now start CoMPaseD at any time by activating the virtual environment and running:

CoMPaseD_gui.py (Graphical Interface)
CoMPaseD_cli.py (Command-Line Interface)