[DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying

[Gregg Helt]

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
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