snakemake

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Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the full installation including all optional dependencies.

Home https://snakemake.readthedocs.io
Versions 3.10.0, 3.10.1, 3.10.2, 3.11.0, 3.11.1, 3.11.2, 3.12.0, 3.13.0, 3.13.2, 3.13.3, 3.4.2, 3.5.1, 3.5.2, 3.5.3, 3.5.4, 3.5.5, 3.6.0, 3.6.1, 3.7.0, 3.7.1, 3.8.0, 3.8.1, 3.8.2, 3.9.0, 3.9.1, 4.0.0, 4.1.0, 4.2.0, 4.3.0, 4.3.1, 4.4.0, 4.5.0, 4.5.1, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 5.0.0, 5.1.1, 5.1.2, 5.1.3, 5.1.4, 5.1.5, 5.2.0, 5.2.1, 5.2.2, 5.2.4, 5.3.0
License MIT
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/snakemake
Links doi: 10.1093/bioinformatics/bts480, biotools: Snakemake

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install snakemake

and update with:

conda update snakemake

docker

A Docker container is available at https://quay.io/repository/biocontainers/snakemake.