- Clone the pangolin repository and cd pangolin
- conda env create -f environment.yml
- conda activate pangolin
- pip install .
- That's it!
Need help troubleshooting your installation? See the pangolin wiki
Dependencies If Not Installing Using the Conda Environment
: 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
- 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*
Check the install worked
Type (in the pangolin environment):
You should see the versions of pangolin and pangoLEARN data release printed respectively.
- If you have previously installed pangolin using pip you will need to update pangolin in the same way, ie pip install .
- Try pip uninstall pangolin and then re-install with python setup.py install