- Clone this repository and
conda env create -f environment.yml
conda activate pangolin
pip install .
- 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.
- If you have previously installed pangolin using
pip, you will need to update pangolin in the same way (
pip install .)
pip uninstall pangolinand then re-install with
python setup.py install