[Gmod-help] Gbrowse/postgresql

Thu Mar 19 08:52:50 EDT 2009

Hi Jean-Pierre,

It looks like I fixed the missing primary_id function yesterday; it's
now in cvs on the stable branch (pre-1.70).

Can I ask what you meant by "Since chado (gmod1.0) does not install"?
Was there a problem I need to fix?

Scott

On Thu, Mar 19, 2009 at 8:18 AM, Gauthier Jean-Pierre
<Jean-Pierre.Gauthier at rennes.inra.fr> wrote:
> Hi,
>
> I'm installing gmod on a new server and have
> a problem connecting gbrowse with my chado/postgresql
> database.
> I am with:
> Red Hat 5
> apache 2.2.3
> postgresql 8.1.11
> gbrowse 1.69 by net-installer.
> Since chado (gmod1.0) does not install, I have made
> a dump restore of our AphidBase (as done during 2008 gmod
> summer school) (see http://www.aphidbase.com/aphidbase --> gbrowse)
> That was gmod0.03 with Gbrowse 1.68 or 1.63
> ....
> Gbrowse works well with yeast.
> That seems ok with porstgres database (same gbrowse config files
> with Bio::DB::Das::Chado adaptator) but tracks are not displayed.
> error_log from apache is given here
> Hy said
> This is not your fault - author of Bio::DB::Das::Chado::Segment should be
> blamed!
> but I have no solution.
> Could somebody help me?
> Jean-Pierre
>
> [Mon Mar 16 09:36:38 2009] [error] [client 193.50.25.62]
> Bio::Graphics::BrowserConfig=HASH(0x20173db0) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:36:50 2009] [error] [client 193.50.25.62]
> Bio::Graphics::BrowserConfig=HASH(0x20173db0) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:36:50 2009] [error] [client 193.50.25.62]
> Bio::Graphics::BrowserConfig=HASH(0x20173db0) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] , referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] -------------
> EXCEPTION: Bio::Root::NotImplemented -------------, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] MSG: Abstract
> method "Bio::PrimarySeqI::primary_id" is not implemented by package
> Bio::DB::Das::Chado::Segment., referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] This is not your
> fault - author of Bio::DB::Das::Chado::Segment should be blamed!, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] , referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Error::throw, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Root::RootI::throw_not_implemented
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/RootI.pm:709, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::PrimarySeqI::primary_id
> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeqI.pm:257, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Graphics::BrowserConfig::make_link
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:3366,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Graphics::Browser::make_link
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:803,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Graphics::Browser::make_href
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:1852,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Graphics::Browser::generate_panels
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:1391,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> Bio::Graphics::Browser::render_panels
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm:882,
> referer: http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> main::detail_panel /var/www/cgi-bin/gbrowse:656, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> main::detail_panel_with_timeout /var/www/cgi-bin/gbrowse:616, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> main::main_display /var/www/cgi-bin/gbrowse:503, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] STACK:
> /var/www/cgi-bin/gbrowse:353, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62]
> ----------------------------------------------------------------, referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
> [Mon Mar 16 09:37:12 2009] [error] [client 193.50.25.62] Use of
> uninitialized value in print at /var/www/cgi-bin/gbrowse line 503., referer:
> http://aphidix/cgi-bin/gbrowse/aphidbase/?name=SCAFFOLD10001
>
>
> --
> Gauthier Jean-Pierre.
> Bio-informatique.
> INRA. UMR BIO3P.
> Domaine de la Motte. BP. 35327.
> 35653 LE RHEU CEDEX.
> tel  : 33(0)2.23.48.51.68
> fax  : 33(0)2.23.48.51.50
> mail : Jean-Pierre.Gauthier at rennes.inra.fr
>
>

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