[ensembl-dev] Manual curation tools

[Matthew Astley]

On Tue, Apr 23, 2013 at 09:22:45AM +0200, Marc Hoeppner wrote:

> [...] one thing I am missing is a tool for inspecting the different
> outputs and progress of the pipeline graphically. The documentation
> suggests Apollo as a useful tool, but I had very mixed results

I think some people do still use it for this purpose, possibly with
locally modified source.

I don't know how Apollo and its Ensembl interface are maintained, but
they have recent activity on their websites.


> [...] it seems to have some problems with some not-so-recent updates
> in the database schema (like the gene_stable_id table, which I think
> was deprecated?)

(According to my notes, but not checking the version history) It was
deprecated in 63 or 64, removed in 65 and the backwards compatibility
views removed in 67.


> Otterlace seems to be an attractive alternative, but I think that
> one is designed to only work within EnsEMBL/Sanger?

Otterlace includes ZMap, Blixem and Dotter.  Together these make the
desktop client part of the application.  Otterlace needs an Otter
Server with associated Ensembl-schema databases to supply the data for
regions to edit.

Both Otterlace and the Otter Server are _designed_ to work anywhere
that can support the necessary databases and webserver back-end.
However the server isn't currently installed anywhere else as far as
we know.

As with any unused software, the ability to work elsewhere is at risk
of becoming vestigial.

> Any way around that and adopt it to my local setup?

With the current state of the Otter code, I suspect it would be more
work to get Otterlace displaying your pipeline output than Apollo.


However ZMap itself should be usable as a stand-alone viewer for gene
builds.  It may not be in a state where you can do this conveniently
now, but it is the direction we are taking it.

If you are interested in this, we should perhaps continue off the
dev at ensembl list.


> I guess my questions is what other people are using - and if there
> is nothing else out there that can talk to an EnsEMBL core DB, what
> I could try to get either of the two options above to work properly.

As developers of Otterlace we need to verify that it is displaying
data correctly.  We tend to look at the ensembl data via SQL or the
API, or the GFF and other underlying data.

I think we may have used Apollo for the purpose, but not recently.

-- 
Matthew Astley
Senior Software Developer
Anacode team, supporting HAVANA