Installation

Ruffus is a lightweight python module for building computational pipelines.

Note

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 https://bunbun68@code.google.com/p/ruffus/ .
  

• Bleeding edge Ruffus development takes place on github:

  git clone git@github.com:bunbun/ruffus.git .
  

• To install after downloading, change to the , type:

  python ./setup.py install
  

Prequisites

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 http://peak.telecommunity.com/dist/ez_setup.py | python

or manually:

wget peak.telecommunity.com/dist/ez_setup.py
sudo python ez_setup.py

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