Python Environment

Python Environment

On a linux/unix machine do:

1. Create genotoscope conda environment with python3.7:

   conda create -n genotoscope_env python=3.7

2. Activate the environment:

   conda activate genotoscope_env

3. Add channels to environment:

   conda config --add channels bioconda

   conda config --add channels conda-forge

4. Install pyvcf and pybedtools through conda:

   conda install pyvcf==0.6.8

   conda install pybedtools==0.8.2

5. Install all other requirements through pip3:

   pip3 install -r genotoscope_env_requirements.txt

6. Only once, download the data for ensembl 75 version (GRCh37) needed to use pyensembl:

   pyensembl install --release 75 --species human

To deactivate the environment use: conda deactivate