[BioRuby] Rakefiles for the Dindel workflow

[Raoul Bonnal]

Hi Hiro,
seems an interesting approach, we could discuss this e-mail tomorrow during the irc meeting.
is it fine  for you ?

I can't catch how do you use pwrake, sorry probably I missed something, I mean the benefit.


On 02/feb/2011, at 04.51, MISHIMA, Hiroyuki wrote:

> Hi all,
> 
> I wrote a rakefile for the Dindel workflow. Dindel is a toolkit to call
> small indels from mapped short-read data (BAM files). See
> http://www.sanger.ac.uk/resources/software/dindel/ .
> 
> The rakefile is available at https://github.com/misshie/RakefileDindel .
> 
> I think my rakefile is a good example of "dynamic task definition".
> During Stage 3 of the workflow, Dindel generates over 300 files for
> exome data. Although the file naming rule is known before running rake,
> the number of files to be generated is unknown at the time.
> 
> van der Aalst et al. (2003) have shown this pattern as "pattern 14:
> multiple instances with a priori runtime knowledge". Rakefiles can
> describe this pattern using Rake::Task#invoke.
> 
> Furthermore, this rakefile demonstrates effectiveness of Pwrake. Stage 3
> is a typical embarrassingly parallel problem.
> 
> To improve rakefile readability, I separated a Rakefile into Rakefile,
> Rakefile.invoke, and Rakefile.helper. Rakefile is workflow description.
> Rakefile.invoke is command-lines to invoke tools. Rakefile.helper has
> helper methods making Rakefile simpler.
> 
> Previously Yannick Wurm has shown a rakefile "cdsToAlignmentToTree" at
> https://github.com/yannickwurm/tidbits/ . The rakefile handles
> exceptions carefully. Mine does not. Yannick's approach is important
> because sometimes error messages in rakefiles are not intuitive.
> 
> So far, my workflow does not use BioRuby at all. Raoul Bonnal have
> suggested BioRuby-rake integration replying Yannick's post. Introducing
> modular task definition to rake is what we need but not very easy
> because each workflow step in a rakefiles is linked too tight.
> 
> Introducing a BioRuby plug-in to support common helper methods
> simplifying rakefiles seems easier. It may contain my Rakefile.helper,
> and Yannick's helper methods and exception handling.
> 
> I will try to write a small plug-in for a while.
> 
> Sincerely yours,
> Hiro.
> -- 
> MISHIMA, Hiroyuki, DDS, Ph.D.
> COE Research Fellow
> Department of Human Genetics
> Nagasaki University Graduate School of Biomedical Sciences
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--
R.J.P.B.