[BiO BB] Announcing "Ruffus": Easy Computational Pipelines in Bioinformatics

[Leo Goodstadt]

A new library called Ruffus is available from
http://ruffus.googlecode.com/svn/trunk/doc/html/index.html.

Ruffus provides easy / lightweight support for running 
computational pipelines in python.

The best way to produce reproducible bioinformatics analyses
is by scripting all the stages or tasks which have to be run.

Ruffus is designed to allow this to happen in python 
in the least intrusive manner possible, and without any
special (non-python) syntax.

Like makefiles (or scons), it helps you to manage
task dependencies. However, because it is designed 
from the start for bioinformatics pipelines (rather than
compiling programmes), no ugly syntax / hacking is
required. 

Ruffus provides automatic support for

   * Managing dependencies
   * Running tasks in parallel
   * Re-starting from arbitrary points, especially after errors
   * Display of the pipeline as a flowchart
   * Reporting


We have been using Ruffus in-house but we would like to see
what other scientists think of the design before we bring
its attention to a wider audience. (We intend to publish 
this as an application note in some bioinformatics journal)

Please help us by sending feedback to:
   ruffus at llew.org.uk


Extensive documentation, download details and two tutorials are
available from http://ruffus.googlecode.com/svn/trunk/doc/html/index.html.


Leo Goodstadt
MRC Functional Genomics Unit
University of Oxford