Snakemake

Snakemake is a pythonic way of writing makefiles.

Snakemake works with distributions like anaconda to package and install dependencies. I recommend using Pyenv to keep things organized and separated out.

Installing

Conda

Snakemake is intended to be used in conjunction with Conda, which is a Python tool that enables installing software both inside and outside of the Python ecosystem.

Regular Python

If you don't need to install dependencies via conda, install snakemake via pip:

pip install snakemake

Links

Projects

Snakemake documentation: https://snakemake.readthedocs.io/en/stable/

Snakemake for Bioconda documentation: https://bioconda.github.io/recipes/snakemake/README.html

Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake

Examples

A SingleCell RNASeq pre-processing pipeline built on snakemake: https://github.com/Hoohm/dropSeqPipe/blob/master/Snakefile