Quick start

This guide will show you the basic usage of SnakeLines pipelines on small toy example. We assume that you have Linux system installed (tested on Ubuntu 16.04.1).

Install required dependencies

Follow installation guides for Miniconda and Snakemake. There is no need to install any other tools manually. All required bioinformatic tools are installed automatically by SnakeLines inside dedicated virtual environments to avoid dependency conflicts with already installed tools.

Download SnakeLines scripts

Use git to download sources

git clone https://github.com/jbudis/snakelines.git
cd snakelines

Alternately you may download sources directly.

Execute pipeline

Toy example read files and references are stored at the /example directory of downloaded sources. Assuming, that sources are downloaded in /usr/local/snakelines, variant_calling pipeline may be executed using

cd /usr/local/snakelines/example/mhv

snakemake \
   --snakefile ../../snakelines.snake \
   --configfile config_variant_calling.yaml