The Snakemake workflow management tool requires Python version 3.4 or higher. Detailed installation instructions can be found in the Snakemake documentation.
bioconda
channel in the list of available channels as explained heresnakemake-minimal
package following these instructions.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.
Verify that Snakemake is installed - this should not produce an error:
$ snakemake --version