[Bioperl-pipeline] xml dir housekeeping

[Shawn Hoon]

Hi Juguang,
	I'm doing some housekeeping. Rite now, the xml directory
is confusing as to which works and which doesn't. I would like to partition the xmls
into working ones and under-dev ones. By working I mean they should have a .t
file and documentation on how to use the pipeline in the xml itself. Right
now, we have blast_file_pipeline.xml cdna2genome_pipeline.xml phylip_tree_pipeline.xml
For the other xmls that we have I would like to put them into bioperl-pipeline/xml/dev
. Also, bioperl-pipeline/xml/debut doesn't seem to belong in the repository, so
I would like to remove it ok?

On writing pipeline tests, pipeline tests should  be file based, meaning
it doesn't assume the availability of biosql or ensembl or other schema. Also
no hardcoding.  Within the xml, one can add the various adaptors and stuff but commented out
for testing purposes. Users who want to use the templates, should make a copy
and uncomment or modify accordingly.

cheers,

shawn





 

	

-- 
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* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
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