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

[Martin Gollery]

I took a look at your site, downloaded the source and went through both
tutorials. The first 5 minute tutorial took me much more than 5 minutes, the
second took me much less!
Anyway, I think that this is the Susan Boyle of bioinformatics- I didn't
expect much out of it because it was not pretty. I am familiar with the
graphic-based pipeline builders like VIBE and Pipeline Pilot, and these are
much prettier. Still, I think that what you have created is very valuable
for at least a couple of reasons.

First, many programmers do not want to use visual 'drag and drop' type
tools. These tools are aimed more at non-programmers, but in my experience
biologists would rather hire someone to create a pipeline anyway.

Second, your module is free and most of the other tools are not. While
something like Pipeline Pilot is a wonderful system in the long run, most
people just want to get something done today, and don't want to spend money
to do it.

Third, if I am creating a pipeline in Python, then your module simply makes
things easier and more efficient. To switch to another system is an extra
learning step that I don't need. Again, people generally want to solve the
problem at hand, not to create another issue.

Fourth, I like the error-checking and restart capabilities because I have
had trouble with that in the past!

Best regards,
Martin Gollery




---------- Forwarded message ----------
From: Leo Goodstadt <leo.goodstadt at dpag.ox.ac.uk>
Date: Mon, Jun 1, 2009 at 7:01 AM
Subject: [BiO BB] Announcing "Ruffus": Easy Computational Pipelines in
Bioinformatics
To: bbb at bioinformatics.org


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


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-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com