[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)
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
More information about the BioRuby
mailing list