Installation
Using Bioconda or Mamba
- Install using conda (or mamba)
conda install -c bioconda -c conda-forge -c defaults pangolin
- Try it out pangolin -h
For development
- Clone the pangolin repository and cd pangolin
- conda env create -f environment.yml
- conda activate pangolin
- pip install .
Need help troubleshooting your installation? See the
pangolin wikiDependencies 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/pangolin-dataYou will need to pip install them alongside the other dependencies for pangolin (full details and versions found in
environment.yml).
Check the install worked
Type (in the pangolin environment):
pangolin -v
pangolin -pv
You should see the versions of pangolin and pangolin-data release printed respectively.
Troubleshooting update
- 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