Project Documentation

Project documentation is available here: http://www.ruffus.org.uk

Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in bioinformatics for managing dependencies in parallel workflows.

The Ruffus provides automatic support for

Managing dependencies
Parallel jobs
Re-starting from arbitrary points, especially after errors
Display of the pipeline as a flowchart
Reporting

Computational pipelines are often conceptually quite simple, especially if we breakdown the process into simple stages, or separate tasks.

Each stage or task in a computational pipeline is represented by a python function.

Each python function can be called in parallel to run multiple jobs.

It was originally written for scientific research (bioinformatics/genome analysis pipelines).

Design goals

(In order)

Elegance
Lightweight
Unintrusiveness
Flexible
Practical (i.e. powerful)

There is no hidden magic so Ruffus is completely customisable.

Installation

sudo pip install ruffus --upgrade

easy_install -U ruffus

Latest Source Code

The latest (unreleased) source code in development can be downloaded from the Google repository here

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

or from the git hub repository:

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

The git hub code tracks the day to day development of Ruffus while the Google repository is slightly more stable.

Tutorial

An simple tutorial is available here: http://www.ruffus.org.uk/tutorials/new_tutorial/introduction.html

Cylindrophis ruffus

Is the name of the red-tailed pipe snake from Hong Kong where the author comes from http://www.ruffus.org.uk/why_ruffus.html#why-ruffus