Requirements

Requirements

pangolin runs on MacOS and Linux. The conda environment recipe may not build on Windows (I haven’t tested it), but can be run using the Windows subsystem for Linux.

  1. Some version of conda, we use Miniconda3. Can be downloaded from here
  2. Your query fasta file

Dependencies

  - pandas>=1.0.1
  - wheel>=0.34
  - joblib>=0.11
  - PuLP>=2
  - scikit-learn==0.23.1
  - biopython=1.74
  - minimap2
  - pip=19.3.1
  - python=3.7
  - snakemake-minimal=5.13
  - pandas==1.0.1
  - usher
  - git+https://github.com/cov-lineages/pangoLEARN.git
  - git+https://github.com/cov-lineages/pangoLEARN.git
  - git+https://github.com/cov-lineages/scorpio.git
  - git+https://github.com/cov-lineages/constellations.git

Recommended to install using conda

Next: Installation