[Bioperl-pipeline] getting your example to work

[shawnh@worf.fugu-sg.org]

Hi Andy,
	yup you caught us right in the midst of dev :)
We should really update the website. Basically what we have been doing
the last two weeks was prety major development on the genome annotation pipeline.
Currently we are running the genewises on the Ciona genome and will be adding protein
annotation to that as well. As you would expect, we had some schema changes,
and lotsa code changes. We didn't branch before this as we felt the pipelines
weren't mature enough being able to do just RepeatMasker->Blast. Instead, now that
we managed to get Genewise incorporated, we have some added functionalities like
filtering and converters that will solve a lot of problems for future pipelines.
 Naturally there is some lag time in the XML dev and its
funny that u mailed us as we just scheduled an XML dev session tomorrow.

> You may want to check your code against a new install of XML parser etc.. to
> make sure it still works.
> I can start switching the use statements, but then I am afraid you may  have a
> call later on that will not work...
> or I can just put Expat.pm where the script thinks it ought to be.  Either way
> you will need to let people know about this if they have to install the XML
> modules

Thanks for the heads up on the XML. We will be considering whether
to continue using the XML parsers or to write our own as we aren't very
satisfied with them in the first place. It will also make it much easier
to package those modules with the pipeline to ease some installation pains.
We will make an annoucement to the list once things stabilizes.

cheers,

shawn


> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC 
> (314) 615-6989
> http://www.oriongenomics.com
> 
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-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************