What is Snakemake

Snakemake is an easy to use workflow management system. Contrary to make, which was designed by computer scientists to build software, snakemake was designed for academic/professional research in Bioinformatics, so it may feel more intuitive for academic users.

Snakemake is a python package - so we can install using the default python installer, pip.

Installing Snakemake

Mac & Linux Users

In a terminal window enter the command:

bash
pip install snakemake

followed by pressing the Return key.

Verify that your installation worked correctly by entering

bash
snakemake --version

into a terminal and pressing Return.

The expected output is the current version on the software, which should be greater than

bash
5.2.2

Windows users

We need one extra step here. In a cygwin window enter the command:

bash
conda install datrie

followed by pressing Return.

If you get an access denied error, you may have not clicked on single user install in the Anaconda installation. De- and re-install Anaconda and try again.

If the above command works, your terminal will look something like this:

bash
The following NEW packages will be INSTALLED:
datrie: 0.7.1
proceed ([y]/n)

Type y and hit enter. Once this is done, type:

bash
pip install snakemake

followed by pressing the Return key.

The expected output is the current version on the software, which should be greater than

bash
5.2.2