[BioRuby] Problem with PAML wrapper

[Marc Hoeppner]

Hi,

now with vers. 1.3 released (congrats on that by the way!), I was hoping 
to speed up some analyses by using the Bio::PAML module. However, I 
can't get it to work...

Ruby info:
ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0]
on a Macbook, Os X 10.5

This is what I tried:

1) read in a fasta file -> to Bio::Alignment::OriginalAlignment
Verified the object (i.e. alingment.each_pair produces what it should, 
so I am assuming that step was successful)
2) read in a newick-type tree (with branch lengths.. ) and converted it 
to Bio::Tree - again, printed it out to see if it worked, and it did.
3) Verified that taxon labels in both files/objects were identical
4) Verified that all the sequences in the alignment were in fact of 
equal lengths

I then tried to use the module as described:

baseml = Bio::PAML::Baseml.new
report = baseml.query(alignment,tree)

-> nothing happens, i.e. program just exists normally, report.to_yaml 
shows an empty object.

In order to confirm that PAML was working and that the data is, in 
principle, compatible with Baseml, I created a normal ctl file and ran 
the whole analysis from command line. And that worked.

So I then tried to do it the less sophisticated way:

baseml = Bio::PAML::Baseml.new
baseml.run(my_local_ctl_file)

Again, nothing happened (should print out the results to the screen, as 
I understand it).

Any suggestions on what I am doing wrong here? I suspect a problem with 
the creation of the temporary folder/files, but frankly don't know 
enough about the details to follow up on that. Also, I would guess that 
such issues were addressed when developing the module (?).

Cheers,

Marc