Setup

Requirements:

• python3

• git

Step 1: Code & Environment

git clone https://github.com/bricoletc/WMS_teaching
cd WMS_teaching

Venv and pip (recommended)

python3 -m venv venv && source venv/bin/activate
pip install -r pip_requirements.txt

Now install bcftools and bgzip. For eg on Debian-like systems: sudo apt-get install bcftools tabix

Alternative: Conda

conda create --name WMS -c bioconda -c conda-forge --file conda-requirements.txt
(Proceed? [y])
conda activate WMS

pip install $(grep "gramtools" pip-requirements.txt)

Step 2: Data

Download this tarball: https://oc.ebi.ac.uk/s/4liZWUYp1kFluCY .

mv /path/to/tarball/WMS.tar.gz ./
tar -xf WMS.tar.gz
cp -r data_WMS/P3/* P3/data
mkdir P2/data P2/data/genomes
cp data_WMS/P2/* P2/data/genomes

The tarball contains the datasets we’ll use in P2 and P3.