Installation

The HUNT-GWAS Pipeline requires Snakemake and the conda package manager. Singularity is optional, but recommended. This page will show you how to install them.

First we will install the conda pacakge manager. Go to https://www.anaconda.com/download/ and select the Python 3+ version.

Then follow the installation instructions.

Next, we will need to install snakemake. We will do this using anaconda.

# install snakemake from the channel bioconda
conda install -c bioconda snakemake

Finally you can install the HUNT-GWAS Pipeline with the command

git clone git@gitlab.com:huntgenes/gwas_pipeline.git

Singularity

Singularity is a way to package software and the operating system it is run on to ensure complete reproducibility. Using it with the HUNT-GWAS pipeline is highly recommended. The installation-instructions are here: http://singularity.lbl.gov/install-linux