Installation

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

Troubleshooting install see the pangolin wiki

Dependencies if not installing using conda environment

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).

Dependencies specific to pangolin 3.0

• pangolin now also has an UShER mode for fast parsimony placement, so requires UShER
• pangolin 3.0 now outputs scorpio calls for VOCs and VUIs*

*VOCs and VUIs: Variants of concern and Variants under investigation

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