[BioRuby] Rake

Matt diapriid at gmail.com
Tue Jan 18 15:21:36 UTC 2011


I like it.  It might be nice to extend your pipeline in a generic
manner (SimpleAnalysisPipeline). Just a couple of steps that would be
extensible/swappable to different software.  The generic pipeline
would "just work" given a minimal local configuration (I like your
starting point).

Swappable/configurable steps might be

Pre-process (trim / quality filters?)
Alignment   (align)
Post alignment (gblocks)
Translation   (to Nexus)
Analysis      (Phyml)

The idea is that we could swap in components (TNT or RaXML for Phyml,
Muscle for MAFFT etc.)- but also that the pipeline remains "simple".

If I find some time I'd like to work on my first attempt at a BioRuby
Plugin, a wrapper for TNT (hopefully tied in to the analysis bit


On Tue, Jan 18, 2011 at 3:56 AM, Yannick Wurm <yannick.wurm at unil.ch> wrote:
> Dear List,
> I'd had a few issues setting up a rake file 2/3 weeks ago. Thanks to Hiro-san and some of the google-able tutorials things are now working.
> It is supposed to be a mini-pipeline that takes a file called "cdsSeq.fasta" and goes through the following steps for tree building:
>  - tranlsation
>  - multiple alignment (mafft)
>  - gblocks to remove crap
>  - tree building (phyml)
>  - codon-level alignment: reverse translated from protein multiple alignment (pal2nal)
>  - gblocks to remove crap
>  - tree building (phyml)
> https://github.com/yannickwurm/tidbits/blob/master/cdsToAlignmentToTree/Rakefile
> It depends on a bunch of stuff in my $PATH, so probably won't run elsewhere out of the box. But FWIW maybe it can be usefull to a random googler.
> However, it feels quite clunky, so I think I should do things differently in the future. If you have any comments or suggestions, I'd be most happy to hear them.
> Cheers,
> yannick
> -------------------------
>  Ant Genomes & Evolution
> http://yannick.poulet.org
>   skype://yannickwurm
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