quickstart.md

Quickstart

1. Clone

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

2. virtualenv OR conda

if using virtualenv:

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

if using conda:

conda create -n env python=3.9
conda activate env

3. Dependendencies

pip install jupyterlab massql reportlab openpyxl matplotlib pyopenms

OR

pip install -r requirements.txt

4. massqlab_config.json

{
  "data_directory": "data/",
  "queryfile": "MassQL_Queries.csv"
}

5. Run

py src\MassQLab_console.py      # Run full pipeline via console

OR

py src\MassQLab_GUI.py          # Launch GUI (if supported)

OR

jupyter lab                     # Launch Jupyter Lab, navigate to notebooks directory and launch MassQLab_notebook.ipynb

6. Results

Results are saved in "MassQLab_Output" directory within data_directory

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