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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

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