[Bioperl-pipeline] Requirements for pipeline installation

[Elia Stupka]

> I can recommend either using the Generic Feature Database, which we are
> refining which currently does allow storing of blast results

but that will not give you a simple way to view the data

> or writing a hacky method that stores into ensembl without the need
> for a contig.

but that will mean you will not be able to have the sequences associated
with the annotation. Also, many calls later rely on having the sequence
available. Imagine you start off by repeatmasking, and then you want to
blast the repeatmasked sequence, if the sequences are in ensembl and the
repeats are in ensembl it's a simple method call to get the repeatmasked
sequence, if not, you have to roll your own code. And the same for anythin
else.

It basically means shooting yourself in the foot.

> I was in the process of writing a pipeline that takes in a fasta file of
> input sequences running a set of blasts and writing to either a GFD or
> ensembl database. If you have your own simple schema that you want, you
> can of course write your own adaptor module and plug that right in.

Of course it's doable, but needs a lot of code to be written at the
moment.... Oh, well up to you...

Elia

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