[Bioperl-pipeline] Starting the pipeline redux

[Elia Stupka]

> So, when you say you guys are working on XML, is it safe to say that
> you are working on an XML schema to describe what a valid pipeline XML
> doc will look like,

The schema has already been agreed. Now when we say we are working on XML
we actually mean writing the filled real templates for real pipelines that
people want. Of course at a later stage this step will be trivial when all
iohandlers, datahandlers, databases,etc are done and dusted, while at the
moment when we write XML templates we also improve the code or write
missing wrappers,etc.

> Also, I wasn't sure of your use cases, either, but have some to
> contribute that are common I am sure.  Along the lines of cron jobs,
> but multi step query and filters things.  I think it was mentioned
> before.

The only thing you would cron-job once you have a pipeline is the pipeline
itself, every x weeks/months. In theory the pipeline will contain all the
analysis you want to do from A to Z. 

You mention filters, that is definitely one area we want to work on, to be
able to apply filters at any stage of the process to the data before it
gets stored or before it gets computed on. We will probably add one soon
to our own pipelines, so I will let you know.

Elia

********************************
* http://www.fugu-sg.org/~elia *
* tel:    +65 6874 1467        *
* mobile: +65 9030 7613        *
* fax:    +65 6779 1117        *
********************************