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sgkit-publication-popgen's Introduction

Popgen

This is a cutdown copy of the code at https://github.com/tomwhite/shiny-train/tree/sgkit/notebooks/gwss

Create environment

mamba env create --file environment-pinned.yml
conda activate sgkit-publication-popgen

Download data

./download-ag1000g-data.sh

Run notebooks

jupyter notebook

Then run the following notebooks:

  • sgkit_import_haplotypes.ipynb
  • sgkit_h12.ipynb

Upate/save environment

The pinned environment file was created with

conda env export -v --override-channels --channel conda-forge --channel defaults --channel=conda-forge/label/broken --name=sgkit-publication-popgen > environment-pinned.yml

sgkit-publication-popgen's People

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