The Snakemake workflow management tool requires Python version 3.4 or higher. Detailed installation instructions can be found in the Snakemake documentation.
biocondachannel in the list of available channels as explained here
snakemake-minimalpackage following these instructions.
In short, Snakemake can be installed either via the
the smaller (but sufficient)
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
$ 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
$ 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.
Verify that Snakemake is installed - this should not produce an error:
$ snakemake --version