Installation

This workflow was designed to use conda for dependency management and utilizes Snakemake as the workflow management system, ensuring reproducible and scalable analyses.

This installation guide is designed for Unix/Linux environments; however, this pipeline has been minimally tested on OSX as well.

Obtain a copy of this workflow

Clone this repository to your local system, into the place where you want to perform the data analysis:

git clone git@gitlab.com:data-analysis5/54gene-wgs-germline.git

Install the run-time environment

If needed, follow this guide to install Miniconda.

Once installed, create the run-time conda environment with minimal dependencies defined using the following command:

conda env create -f environment.yaml

Activate the environment as follows:

conda activate 54gene-wgs-germline