connect gbrowse to drupal db

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connect gbrowse to drupal db

Sofia Robb
-- sorry if this message comes thru a few times, I forgot which email address I am registered under for the the mailing list.



Hello,

I am trying to connect gbrowse to my drupal chado database but I am unsuccessful. What am I missing? 

I created the user nobody with the following commands:

CREATE USER nobody;
ALTER USER nobody WITH PASSWORD 'nobody';
GRANT CONNECT ON DATABASE drupal TO nobody;
GRANT USAGE ON SCHEMA chado TO nobody;
ALTER ROLE nobody SET search_path TO chado;


and have this in my config:

[main:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=drupal
                -user nobody
                -pass nobody
                -srcfeatureslice 1
                -inferCDS 1
                -organism "Schmidtea mediterranea"

and I am getting this error:

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: trying to find SOFA STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486 STACK: Bio::DB::Das::Chado::sofa_id /usr/local/share/perl/5.18.2/Bio/DB/Das/Chado.pm:886 STACK: Bio::DB::Das::Chado::new /usr/local/share/perl/5.18.2/Bio/DB/Das/Chado.pm:252 STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/share/perl5/Bio/Graphics/Browser2/DataBase.pm:44 STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/share/perl5/Bio/Graphics/Browser2/DataSource.pm:1005 STACK: Bio::Graphics::Browser2::Render::region /usr/share/perl5/Bio/Graphics/Browser2/Render.pm:1116 STACK: Bio::Graphics::Browser2::Render::segment /usr/share/perl5/Bio/Graphics/Browser2/Render.pm:1197 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/share/perl5/Bio/Graphics/Browser2/Render.pm:1932 STACK: Bio::Graphics::Browser2::Render::update_state /usr/share/perl5/Bio/Graphics/Browser2/Render.pm:1922 STACK: Bio::Graphics::Browser2::Render::run /usr/share/perl5/Bio/Graphics/Browser2/Render.pm:296 STACK: /usr/lib/cgi-bin/gbrowse/gbrowse:50 -----------------------------------------------------------

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