gapsnake

gapsnake is a snakemake-based workflow for the reconstruction of genome-scale metabolic models using gapseq. It is designed for cases where models for several (from a few to thousands) prokaryotic genomes are reconstructed with the same workflow. It aims to combine an easy and quick usage with full customizability of each individual gapseq module.

Prerequisites

• you will need to have gapseq and its dependencies installed. Also, make sure that you have gapseq in your PATH variable.

Installation

# Cloning the development version of gapsnake
git clone https://github.com/Waschina/gapsnake
cd gapsnake

# Create and activate a conda environment "gapsnake"
conda env create -n gapsnake --file gapsnake_env.yaml
conda activate gapsnake

Setting up cluster execution

Note: Until now, only tested with the SLURM scheduler on CAU's caucluster.

conda activate gapsnake
cookiecutter --output-dir ~/.config/snakemake https://github.com/metagenome-atlas/clusterprofile.git

Quick start

Local machine

# The Setup
cd /path/to/project/directory # Usually one dir up from where your genomes are
conda activate gapsnake
export PATH="${PATH}:/path/to/gapsnake/"

# Initialize gapsnake run
gapsnake init genomes/ # or instead of "genomes/" any path the place where your genomes are

Cluster execution

gapsnake recon --profile cluster