[Bioperl-pipeline] XML GLobal Variables

[Shawn Hoon]

Hi Folks,
	its been quiet on the development front  lately..I'm currently working 
to provide a tarball release
of various that various packages that people can download and setup. 
The packages should include the following:

bioperl-live 1.2.1
biosql release 1-0-0
bioperl-db relese 1-1-0
ensembl-12-1
bioperl-pipeline MAIN
bioperl-run MAIN

along with a data directory probably.


I proposing making an addition to the  XML templates and XML Importer. 
To minimize the number of
modifications one has to change for working directory paths, lets allow 
variables to be set. I don't wish to
go into XSLTs and stuff. I propose a solution that allows minimal code 
changes:

in each XML file have an additional tag:

<pipeline_setup>
   <global workdir="t/data/"
	       datadir="/data/"
	       anyvar="my_txt"/>

<database_setup>
     <streamadaptor id="1">

...snip...
     <iohandler id="1">
       <adaptor_id>1</adaptor_id>
       <adaptor_type>STREAM</adaptor_type>
       <iohandler_type>OUTPUT</iohandler_type>
       <method>
         <name>new</name>
         <rank>1</rank>
         <argument>
           <tag>-dir</tag>
           <value>$workdir/cdna2genome_results</value>

...snip...

All variables with "$" will be replaced with the values in the global 
tag.
. We can also  any variables besides paths, like
$blastparam etc...hopefully this removes confusion as to what one has 
to change to suit his
env.

changes are made and tests passed. Kiran and others pls comment. I will 
commit it tomorrow.

cheers,

shawn