[Bioperl-pipeline] new xml setup

[Shawn]

I have refactored the xml setup, merging the three files into one. 
Quite simply, the file is setup as follows:

<pipeline_setup>
  <database_setup>
  <iohandler_setup>
  <pipeline_flow_setup>
  <job_setup>(optional)
</pipeline_setup>


so running and writing it is easier. For reusing of the dbadaptors and
iohandlers, the idea is that we have two xml libraries containing all
these adaptor moules and their method calls respectively. Juguang's
pipeline creator will read these two files and they will provide the
designer the available modules and method calls. This creator will then
generate the XML file with all the required modules and methods, a self
contained xml file without the need to  link  xml files. 
For an example of this file, take a look a the pipeline_setup in
genomic_sequence_annotation/pipeline_setup.xml

This pipeline requires the following packages:
bioperl-run
bioperl-pipeline
ensembl (revision 4-1)
BioToEns (which we might want to move to a converter dir inside
bioperl-pipeline)

I have also reworked Xml2Db.pl to work with this. I have removed the
hardcoded path to XML::SimpleObject. Thus to use the script, you will
need install and point your perl5lib to  it.

Do we want to include this module as in our distribution as well? Saves
people the need to install it? We might be modifying it for our own
purposes...

Next order of business is to provide a tarball for an example of this
pipeline where people can use to run repeatmask and blast on an ensembl
database.

this was a lot less work than it seems :)
I will put more of the docs on the website.

comments?

shawn