[Bioperl-pipeline] XML GLobal Variables
Shawn Hoon
shawnh at fugu-sg.org
Thu Apr 10 23:33:53 EDT 2003
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
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