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Python Environment
Damianos P. Melidis edited this page Nov 25, 2021
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On a linux/unix machine do:
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Create genotoscope conda environment with python3.7:
conda create -n genotoscope_env python=3.7
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Activate the environment:
conda activate genotoscope_env
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Add channels to environment:
conda config --add channels bioconda
conda config --add channels conda-forge
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Install pyvcf and pybedtools through conda:
conda install pyvcf==0.6.8
conda install pybedtools==0.8.2
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Install all other requirements through pip3:
pip3 install -r genotoscope_env_requirements.txt
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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