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 Windows

• Launch Anaconda navigator
• Add bioconda channel in the list of available channels as explained here
• Install snakemake-minimal package following these instructions.

Installation on Linux and macOS

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

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

If your installation fails with: Failed building wheel for datrie.
it should work to install datrie first:

$ conda install datrie

Conda may be slow to resolve the dependencies and sometimes fails to select a recent release of snakemake. If installing snakemake with conda is taking very long, or if it installs an old version (below 5.0), a solution can be to use mamba:

$ conda uninstall snakemake # to remove a pre-5.0 version of snakemake
$ conda install -c conda-forge mamba
$ mamba install -c conda-forge -c bioconda snakemake

For further details, see the latest installation instructions.

How to verify the installation

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

$ snakemake --version