[Bioperl-pipeline] Re: Forester in Biopipe

[Shawn Hoon]

No, there is no support for this currently. Writing a wrapper for this 
application in bioperl-run which is in java I believe will be a way to 
start.
See there is a bunch of treeio support in bioperl, handling the I/O 
should be quite easy. Once you have the wrapper then you can integrate 
this into biopipe
quite easily.
Pls look at some of the wrappers in bioperl-run that work on java apps, 
mainly : Bio::Tools::Run::Eponine and Bio::Tools::Run::Vista for a 
start.

let me know if you have any more questions.

cheers,

shawn

On Wednesday, December 17, 2003, at 10:00AM, Mathieu ROUARD wrote:

> Hi,
>
> I've just had a look at your Biopipe. It is very interresting for my 
> works.
> I'm thinking in developping one for my own work, but I would like to 
> know if
> it's possible to insert to it the FORESTER package. I haven't found 
> any of
> the modules about FORESTER (SDI DORIO)in the Biopipe website. Will the
> FORESTER modules be developed for BIOPIPE? Is it difficult and long to 
> do
> it?  FORESTER is a very interresting package, and I think it il will be
> usefull to insert it in biopipe.run...
>
> Yours sincerely,
>
> Mathieu Rouard
>
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