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

[Paulo Nuin]

You just forgot to mention that it's Python 2.6 compatible only.

Paulo

On 1-Jun-09, at 10:01 AM, Leo Goodstadt wrote:

> 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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