[flymine-dev] FlyMine GBrowse questions

[Kim Rutherford]

On Thu, 21 Feb 2008 11:19:55 +0100, Wolfgang Lugmayr wrote:

> hi,
> we have flymine 11 running at our site without the gbrowse support.

> we can access the gbrowse flymine 11 data at our url:
> http://flymine/cgi-bin/gbrowse/flymine-release-11.0/
> and it seems fine.

> but in the flymine application we see only the url:
> e.g. zen
> http://flymine/?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750
> instead of 
> http://flymine/cgi-bin/gbrowse/flymine-release-11.0?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750
> or 
> http://flymine/cgi-bin/gbrowse_details/...

> do i miss some configuration settings during the build somewhere?

Hi.  Sorry for the problems.  The documentation wasn't good for GBrowse
configuration.  The problem you are seeing is probably due to a
mis-feature which means that the GBrowse properties need to be in
build.properties.<mine> and in build.properties.<mine>-gbrowse.

These are the properties you'll need in both files:
  gbrowse.database
  gbrowse.database.adaptor
  gbrowse.database.source
  gbrowse.database.host
  gbrowse.database.user
  gbrowse.database.password
  gbrowse.database.write.user
  gbrowse.database.write.password

This has been fixed in trunk so that build.properties.<mine>-gbrowse
isn't needed anymore - all properties will go in build.properties.<mine>.

I've updated http://www.intermine.org/wiki/GBrowseConfiguration so I
hope it will be clearer for others.

Kim.