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 20.04).

Install required dependencies

Follow installation guides for Miniconda. 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.

Installation as a Conda package

# In order for SnakeLines Conda virtual environments to work, user has to add several Anaconda repository channels to Conda.

conda config --add channels bioconda
conda config --add channels g2554711
conda config --add channels g2554711/label/bioconda
conda config --add channels conda-forge
conda config --add channels agbiome
conda config --add channels rsmulktis
conda config --add channels moustik

conda install mamba -n base -c conda-forge

mamba create --name snakelines-env -c bioconda snakelines
mamba activate snakelines-env

Alternately you may download sources directly.

Execute example pipeline

Toy example read files and references are stored at the /example directory of Snakelines package in conda installation directory. To access them, simply use command below to copy them out of conda directory:

cp -R `conda info --base`/envs/snakelines-env/share/snakelines/example snakelines-examples

variant_calling pipeline may be executed using:

mamba activate snakelines-env

cd snakelines-examples/genomic

snakelines \
   --configfile config_variant_calling.yaml \
   --use-conda \
   --cores 2