[Biojava-l] Running apps with Java

[Martin Senger]

> Isn't this what the ACD files in EMBOSS are doing? Perhaps not 
> reinventing the wheel would be good? Admittedly ACD is not the most 
> parsable file format to work with, but we have an XML dialect of it 
> which is (part of Martin's Soaplab).
> 
> Martin - is the XML schema available somewhere? I can't find it from 
> the webpage...
>
   Yes, it's here: 
http://industry.ebi.ac.uk/applab/home/metadata/AppLabAnalysis.dtd

   And I would add to this:
 
> > I do not think it
> > would be too hard to come up with an XML schema for describing how programs
> > should be run.
>
   ...that it may not be the high-level science but it is not completely
easy either. I have spent long time (starting with the W2H project, 
through Applab project and now in the Soaplab) to find what are all 
reasonably possible combinantions of the command-line parameters. So let 
me know if I can be of any help if you decide to go this way...

   Regards,
   Martin

-- 
Martin Senger

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