[Bioperl-l] question about the nature of bioperl

[Elia Stupka]

> bioperl-pipeline and bioperl-run, create an empty database, load one of
> the xml files provided, modify to decide what input you want to have
> (anything you can provide an adaptor for), modify to decide where you want
> to write the output, run the PipelineManager.pl and it should all work
> neatly....

Sorry should have mentioned that the xml files are what we are working on
at the moment, so far as a test you can try one which does a simple
repeatmask followed by a few blasts. This one will be growing in the next
days and weeks, until the xml represents a full ensembl-style
annotation. The other xml file we are working on is one to take proteins
from different genomes, cluster them using TribeMCL and genreate families
then convert those into ensembl families. These two are in the works at
present, as soon as they are out we should be working on xml templates for
EST clustering using STACK and for assembly of reads into contigs using
phrap, etc.

Now, that is a clearer picture, that doesn't put anybody's a** on the
line... :)

Elia

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