setup_guide.md

Setup Guide

Follow these steps to set up a virtual environment and install dependencies for MassQLab. (Or see Quickstart)

1. Download the Project

Option A: Clone with Git
(Requires Git to be installed)

git clone https://github.com/JohnsonDylan/MassQLab.git
cd MassQLab

Option B: Download ZIP from GitHub

1. Go to github.com/JohnsonDylan/MassQLab
2. Click the green "Code" button → "Download ZIP"
3. Extract the ZIP and open a command prompt in the extracted MassQLab folder

2. Check Python Installation

Run:

py --list

Make sure Python 3.9 is listed. If not:

• Install Python 3.9 from: https://www.python.org/downloads/
• During installation, check the box "Add Python to PATH"

If you get an error, Python may not be installed or not added to your system path.

3. Use virtualenv OR conda environemnt

3.A. Create and Activate a Virtual Environment

Ensure virtualenv is installed

pip install virtualenv

Navigate to the project directory:

cd path\to\MassQLab

Create and activate the virtual environment:

py -3.9 -m venv env
env\Scripts\activate

You should now see (env) at the start of your terminal prompt.

3.B. Create and Activate a Conda Environment

Ensure Anaconda is installed https://www.anaconda.com/docs/getting-started/anaconda/install

Navigate to the project directory:

cd path\to\MassQLab

Create and activate the conda environment:

conda create -n env python=3.9
conda activate env

You should now see (env) at the start of your terminal prompt.

4. Install Dependencies

The following may be sufficient:

pip install jupyterlab massql reportlab openpyxl matplotlib pyopenms

Otherwise use:

pip install -r requirements.txt

You're now ready to use the notebooks in notebooks/ or run the workflow using provided scripts.

---