Install pangolin

1. Clone this repository and cd pangolin
2. conda env create -f environment.yml
3. conda activate pangolin
4. python setup.py install
5. That’s it

Troubleshooting install see the pangolin wiki

Note: we recommend using pangolin in the conda environment specified in the environment.yml file as per the instructions above. If you can’t use conda for some reason, bear in mind the data files are hosted in a separate repository at

• cov-lineages/pangoLEARN
  you will need to pip install them alongside the other dependencies for pangolin (details found in environment.yml).

Check the install worked

Type (in the pangolin environment):

pangolin -v
pangolin -pv

and you should see the versions of pangolin and pangoLEARN data release printed respectively.

Troubleshooting update

• If you have previously installed pangolin using pip, you will need to update pangolin in the same way (pip install .)
• Try pip uninstall pangolin and then re-install with python setup.py install

Next: Updating pangolin