[Bioperl-pipeline] Requirements for pipeline installation

[Elia Stupka]

> the actual sequence is not stored in the input object and that it would
> have to go and grab it at some point.
> So somehow it has to find it, I am thinking even and indexed fasta file
> would suffice..correct? 

You are absolutely right. You can grab sequences from fasta files using
one of the indexers such as Bio::DB::Fasta. The only thing is that since
anyway at a later stage you don't want to store just the annotation but
the sequences too it's much easier to start off by loading the sequences
into a database. We are also working on other storage places such
bioperl-db + GFD using GMOD as a viewer, we suggested ensembl because that
is totally stable now, while the others are in development.

> Sorry for all the e-mails, yesterday was just one of those days where
> nothing made sense :)

I know the feeling, it would all be so much easier if we were sitting in
front of a terminal and could help you there....

> so that is why I am looking at the code.  I plan on making the first
> test/attempt on a local machine ( I dont want to even think about talking
> to our queuing system)! :)

Well actually the queuing system is the easiest part. Are you using LSF or
some other system? If it's LSF it should really be plug and play.

> I guess i only need info on how to set up reading in flat files and
> setting up a simple database to store results

Basically the example we've put up is exactly what you want to do. As I
say you can read from fasta files by specifying Bio::DB::Fasta as a
streamadaptor, but then you woulnd't have the sequences stored, just the
annotation....

Elia

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