[Bioperl-pipeline] very simple example for pipeline?

[Elia Stupka]

> I noticed in the example you have on teh web page one would need more
> modules etc...and this is confusing me even more.  I am still not sure
> if it is required to have a mySQL database with your sequences inorder
> to load the pipeline.

Basically it is entirely up to you where you want the sequences to come
from and the annotation to go to, at the moment the example we have
provided is based around an ensembl database because it's an easy place to
store both annotation and sequences. You could keep the sequences in
flatfiles or in bioperl-db, however you would still need a place to store
genes, blast hits,etc. so not sure what you would prefer. I really think
ensembl is the "easy way out" because it is specifically geared towards
annotation. The example is really not too complicated, all it adds is an
ensembl database which means basically cvs'ing out the code, and creating
an empty database that's all... we are trying our best to make it as easy
as possible for a newcomer, and will welcome anyway you think we can make
it even easier.

> I have been looking at some of the scripts as well. Something I noticed,
> load_biosql.pl may not work anymore
> since you have calls like Bio::DB::SQL.. and the bioperl-db i checkout has
> your stuff in Bio::DB::BioSQL Bio::DB::SQL doesnt have anything in it.

hmmm.... let us check that....

Elia

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