[Open-bio-l] bio-pipeline schema in

[Keith James]

>>>>> "Elia" == Elia Stupka <elia@fugu-sg.org> writes:

    Elia> Hello, I've just committed our first stab at the schema for
    Elia> the new bio-pipeline.  I will soon import the
    Elia> bioperl-pipeline CVS module, where we will work on the
    Elia> perl-port of the pipeline, trying to please both the generic
    Elia> bioperl user who might want to use it to fetch some
    Elia> sequences from GENBANK and run them through his pipeline as
    Elia> well as gradually porting some (hopefully) all of the
    Elia> ensembl pipeline to this schema.

I'll be sure to have a look at this. Right now I'm working on a
job-running system for our group which is open-sourced. Our needs were
slightly different from those of Ensembl (e.g. we have lots of small,
heterogenous projects each of which do things differetly), so direct
use of the pipeline wasn't possible.

It would be good if we could operate off any open-bio schema as well
as our own, so I'll try to make that possible.

Our current schema, Java data access objects (DB adapters) and running
code, class and schema diagrams are in anon cvs at the Sanger
(http://cvs.sanger.ac.uk) under Pathogen/psu/jobcontrol. The
functional spec and design spec are under Pathogen/psu/docs/sgml in
DOCBOOK sgml as jobcontrol-fspec.sgml and jobcontrol-dspec.sgml.

It currently launches command lines with correct dependencies. It's by
no means finished (target date < 4 weeks).

I'm at the Biojava bootcamp right now, so I'll have to read up
later...

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK