Quickstart

This quickstart guide will walk you through setting up Pankegg, running the pipeline on test data, and launching the web application to explore your results.

Install Pankegg and Dependencies

Install Pankegg via pip, conda, or pixi.
See the Installation section for detailed options.

wget https://github.com/RVanDamme/PANKEGG/archive/refs/heads/master.zip
unzip master.zip
cd PANKEGG-master
pip install .

Download Example Test Data (optional)

Download and extract the example dataset:

wget https://osf.io/5v3zc/download -O pankegg_test_data.zip
unzip pankegg_test_data.zip

Build the SQL Database (optional)

Generate a Pankegg database from the provided CSV using the included test data (for both Sourmash and GTDB-TK classification):

python pankegg_make_db.py -i pankegg_test_data/sourmash_example.csv -o test_sourmash --output_dir pankegg_test_data

Launch the Web Application

Start the web server using the database present in the repository:

python pankegg_app.py --d data/pankegg.db

or use the the database you generated in point 3:

python pankegg_app.py --d pankegg_test_data/test_sourmash

Open web browser

Now, open your web browser and go to the IP address written in your terminal ( http://0.0.0.0:5000) to interactively explore your metagenomic data!