Snakemake

The Snakemake workflow management tool requires Python version 3.4 or higher. Detailed installation instructions can be found in the Snakemake documentation.

Installation on Linux, macOS, and Windows

In short, Snakemake can be installed either via the snakemake or the smaller (but sufficient) snakemake-minimal package.

On Windows, you have to use snakemake-minimal. On Linux and macOS snakemake-minimal is enough unless you want to be able to plot dependency graphs.

To install one of these into a conda environment, type:

$ conda install -c bioconda -c conda-forge snakemake
# or
$ conda install -c bioconda -c conda-forge snakemake-minimal

or, alternatively, if you prefer pip over conda:

$ pip3 install snakemake
# or
$ pip3 install snakemake-minimal

This may fail with an error message containing Failed building wheel for datrie.
If this happens, it should work to install datrie first:

$ conda install datrie

How to verify the installation

Verify that Snakemake is installed - this should not produce an error:

$ snakemake --version