Setting up the environment

Introduction

Some preparations are required before downloading the GENIE data and creating additional auxiliary files needed by the genie package. Please follow the instructions below to set up your environment.

Install mamba

If you haven't done so already anyway, please install mamba, the next generation replacement for conda. One of the advantages of mamba is that it is much faster than conda.

Please see the Mamba Installation Instructions on how to install mamba.

Create a virtual environment for genie

Create and activate a virtual environment

mamba create -n genie
mamba activate genie

Install genie package

mamba install python pandas sinfo
pip install "git+https://github.com/Bayer-Group/genie.parser.git#subdirectory=genie"

Install packages and programs

Install packages

Installation

mamba install -c bioconda bcftools samtools
pip install synapseclient

Install Illumina Annotator and nirvanaparser module

For the normalization and annotation of mutations from GENIE, a working setup of the Illumina Annotator (a.k.a. Nirvana) and the in-house developed nirvanaparser model is needed. Setting up this environment is beyond the scope of this document, please see the documentation of nirvanaparser for instructions.