[Bioperl-l] pipeline

[Elia Stupka]

(Apologies for the cross-post)

We are going to be working with Jason on getting Trees,Alignments,etc. to
work more and more in bioperl and bioperl-db. At the same time, this is
part of our in-house development of synteny stuff in compara, and ideally
we would like to run all of these with ensembl-pipeline.

As we rely entirely on bioperl-db for our sequence handling, and as I am
keen to see more going into bioperl, we are now bound to get a better
runnable system in bioperl and runnabledb system in bioperl-db.

No need to say more, basically I think soon we would have considerable
overlap between these things, and I am thinking whether since we are
thinking of a revamp for the pipeline we shouldn't just think of an
open-bio pipeline that ensembl can use but that is not ensembl dependent.

I can imagine that porting the actual ensembl gene build,etc over would be
crazy initially, but at least most new developments could start in a fresh
system that works on both easily.

What do people think? A bioperl-pipeline cvs module that uses bioperl and
bioperl-db? The nice thing about bioperl-db is that it already inherently
supports multiple biodatabases within it, which will make it much easier
to work with cross-species comparisons,etc.

My initial step will be to do this alignment,etc. stuff in bioperl and
bioperl-db, but I'd be glad if we could paint the big picture as well.

Elia

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