Using Bioconda

  1. Install using conda (or mamba) conda install -c bioconda -c conda-forge -c defaults pangolin
  2. Try it out pangolin -h
  3. That's it!

For development

  1. Clone the pangolin repository and cd pangolin
  2. conda env create -f environment.yml
  3. conda activate pangolin
  4. pip install .
  5. That's it!
Need help troubleshooting your installation? See the pangolin wiki

Dependencies If Not Installing Using the 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

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

Check the install worked

Type (in the pangolin environment):

pangolin -v
pangolin -pv

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

Troubleshooting update