Ruffus is a lightweight python module for building computational pipelines.


Ruffus requires Python 2.6 or higher or Python 3.0 or higher

The easy way

Ruffus is available as an easy-install -able package on the Python Package Index.

sudo pip install ruffus --upgrade

This may also work for older installations:

easy_install -U ruffus

See below if eady_install is missing

The most up-to-date code:

  • Download the latest sources or

  • Check out the latest code from Google using git:

    git clone .
  • Bleeding edge Ruffus development takes place on github:

    git clone .
  • To install after downloading, change to the , type:

    python ./ install


Installing easy_install

If your system doesn’t have easy_install, you can install one using a package manager, for example:

# ubuntu/linux mint
$ sudo apt-get install python-setuptools
$ or  sudo yum install python-setuptools

or manually:

sudo curl | python

or manually:

sudo python

Installing pip

If Pip is missing:

$ sudo easy_install -U pip

Graphical flowcharts The most up-to-date code:

Ruffus relies on the dot programme from Graphviz (“Graph visualisation”) to make pretty flowchart representations of your pipelines in multiple graphical formats (e.g. png, jpg). The crossplatform Graphviz package can be downloaded here for Windows,

Linux, Macs and Solaris. For Fedora, try
yum list 'graphviz*'
For ubuntu / Debian, try
sudo apt-get install graphviz