Snakemake

Snakemake is an easy to use workflow management system. It will allow us to control the execution of a set scripts by by running them from the command line. We will use make to automate the execution of our research projects with a "single click" so that our entire work flow is reproducible.

Snakemake is a Python package - so you will need Python installed on your computer. We recommend installing Python from Anaconda.

Mac & Linux Users:

In a terminal window enter the command:

pip install snakemake

followed by pressing the Return key.

Verify that your installation worked correctly by entering

snakemake --version

into a terminal and pressing Return.

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

5.2.2

Windows users

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

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:

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

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

pip install snakemake

followed by pressing the Return key.

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

5.2.2