
Install pangolin
Install pangolin
- Clone this repository and
cd pangolin
conda env create -f environment.yml
conda activate pangolin
python setup.py install
- 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 withpython setup.py install