[BioRuby] Rake

Raoul Bonnal bonnalraoul at ingm.it
Thu Jan 20 09:13:20 UTC 2011

Dear Yanninck,
rake usually is used inside a project directory to provide common operations to the project.
Which is the idea behind "rake for bioinformatics" ? I mean, you have to copy you rake file where your data are.

Looking at the code there are a lot of dependencies from command line softwares and that could be a problem in maintainability
What about spend some energy on wrapping that commands into BioRuby classes?
In that way those application could be available to other scripts.

If you want to keep the rake approach we should find a way to not replicate rakefiles.
One idea could be to create a rakefile in your working directory, similar to Rails:

# Add your own tasks in files placed in lib/tasks ending in .rake,
# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.

require File.expand_path('../config/application', __FILE__)
require 'rake'

#The user needs just to add  the tasks he wants:

On 18/gen/2011, at 09.56, 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)
> - 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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