[BioRuby] NGS, transcriptome, workflows

MISHIMA, Hiroyuki missy at be.to
Tue Dec 21 14:29:02 UTC 2010

Hi all,

I would like to say something about workflow automation in Ruby.

Recently I am interested in using Parallel Workflow extention for Rake
(Pwrake) for NextGen sequencer data processing. As you may know, Rake is 
Ruby Make, a build tool.

Pwrake is developped by Masahiro Tanaka at University of Tsukuba. He is
also the author of "NArray", very fast matrix calculation engine for
Ruby. Although Pwrake and regular Rake are compatible in syntax, Pwrake
automatically detects workflow steps that can be run in parallel.

Pwrake's parallelization model is "process based". Because I am just a
*user* of bioinformatics packages (like BWA/GATK/DINDEL etc..), it is
what I need.

Pwrake invokes processes via ssh and supports the Gfarm large-scale
distributed filesystem. Of course, it works well on a multi-processor
Linux box.

Although Pwrake is developed for astronomy science, its goal is also
common in bioinformatics.

I think that some helper methods may simplify Rakefiles for 
bioinformatics, and such helper methods are good for a BioRuby plugin.

Pwrake on github:

Presentation at RubyConfX:

Presentation at PRAGMA18:


Raoul Bonnal wrote(2010/12/21 21:33):
> Hi all, I read in the irc's log that a lot of the memebers are or
> will start working on ngs data. I'll re-start ( I worked on 454) with
> the Illumina platform, in few week, do you have some consolidate
> workflow to follow for transcriptome analysis ?
> papers, blogs, etc.. everything is ok :-)
> I'm also interested about the workflow discussion but... are the
> workflow intended to let the not bioinformaticians analyze complex
> datasets or automate some tedious and repetitive task that we
> (bioinformaticians) must do every time ? In both cases our life will
> be probably better :-)
> -- Ra
MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences

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