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Installing Snakemake

Also see the installation page of the Snakemake documentation.


Before you can install Snakemake, you will need to install Python.

I recommend pyenv, which provides a very simple and graceful solution to the problem of managing multiple versions of Python on a single machine.

The creators of pyenv also provide pyenv-installer, which enables the installation of pyenv with a single command.

Also see how-do-i-pyenv.

Installing Snakemake from Pypi with Pip

Once you have Python installed, you should have pip available as well. Snakemake can be installed using pip:

$ virtualenv -p python3 .venv
$ source .venv/bin/activate
$ pip install snakemake

Installing Snakemake from Bioconda with Conda

If you are using conda, you can install Snakemake using conda by first adding some conda channels, then installing Snakemake using conda install: