[Gmod-help] Gbrowse/postgresql

Thu Mar 19 08:18:29 EDT 2009

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 