[BioRuby] Rake

Michael Barton mail at michaelbarton.me.uk
Tue Jan 18 15:17:08 UTC 2011

Hi Yannick,

I think it's a great idea to generate predefined pipelines for common
bioinformatics tasks. I experimented with a tool called Boson six months ago.
It could be worth looking if you feel like investing more time into your

Boson commands, similar to rake tasks, are more modular and can be installed
from the web into a ~/.boson directory. This has obvious advantages over
a single rake file. Boson tasks can be chained together where the data is
passed around in YAML format.

The github link is - https://github.com/cldwalker/boson


Michael Barton

On Tue, Jan 18, 2011 at 03:56:26PM +0700, Yannick Wurm 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)
> AND - 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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