Re: Help in connecting gbrowse to chado

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Re: Help in connecting gbrowse to chado

Scott Cain
Hi Nipun,

I'm cc'ing this to the Tripal mailing list so it can be archived for
future users.

When you use Tripal to install Chado, Chado gets put in its own schema
(named "chado") rather than in the default public schema, so that the
Tripal/Drupal database stays separate from the Chado database.  In
order for the GBrowse adaptor to talk to the Chado database, the user
that you put in the config file has to have its search_path altered so
that it looks in the chado schema before looking in the public schema
(right now, it's looking the the public/Tripal schema, which is why it
can't find SOFA (and I should change that error message to say "SO"
instead, but that is not important)).  The method for doing that is
described here:

  http://tripal.sourceforge.net/?q=node/18

Use the method in the last bullet point for permanently changing the
user's search_path.  You might want to create a separate user for
accessing Chado through GBrowse, since the "tripal" user that you're
using now might still need to see the Tripal/Drupal schema.

Scott


On Thu, Apr 26, 2012 at 5:35 PM, Nipun <[hidden email]> wrote:

> Hi Scott,
>
> Appreciate your guidance on Apollo.
>
> Currently, I am working on configuring GBrowse to work with my
> Chado-Post-Gre installation. These are the first few lines of the
> tripal_demo.conf file (tripal_demo is the name of the database with
> the chado schema containing some pre-loaded features) in the
> gbrowse.conf folder:
>
> [GENERAL]
> description   = Insect Genomes
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -adaptor Bio::DB::Das::Chado
>                -dsn dbi:Pg:dbname='tripal_demo';host='localhost'
>                -user 'tripal'
>                -pass 'tripaldemo'
>
> When I try to access the database via my server by entering
> http://localhost/cgi-bin/gbrowse/tripal_demo/
>
> I get the following error message:
> An internal error has occurred
>
> Could not open database.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: trying to find SOFA
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472
> STACK: Bio::DB::Das::Chado::sofa_id
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:843
> STACK: Bio::DB::Das::Chado::new
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:242
> STACK: Bio::Graphics::Browser::Util::open_database
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser/Util.pm:187
> STACK: /usr/lib/cgi-bin/gbrowse:180
> -----------------------------------------------------------
>
>
> Generic genome browser version Bio::Graphics::Browser=HASH(0x25dd4d0)
>
>
> I am thinking it has to do with these files:
>
> % cat sequence-gff-views.sql   | psql <Chado-database-name>
>  % cat sequence-gff-funcs.pgsql | psql <Chado-database-name>
>
>
> How do I exactly cat and pipe with the psql commands?
>
> Thanks and regards,
> Nipun



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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