[BioRuby] Rake

Yannick Wurm yannick.wurm at unil.ch
Tue Jan 18 08:56:26 UTC 2011

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)


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. 



 Ant Genomes & Evolution 

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