[Gmod-help] Gbrowse/postgresql
Scott Cain
scott at scottcain.net
Thu Mar 19 10:14:08 EDT 2009
Hi again Jean-Pierre,
I should have mentioned, especially since you wrote that you used the
net installer to get 1.69, that you can use the net installer to get
cvs checkouts as well. Just rerun the installer and add the '-d'
flag, like this:
sudo perl gbrowse_netinstall.pl -d
and it will get the "development" versions of both BioPerl and
GBrowse. In this case, the development version means the 1.70
prerelease, not GBrowse 2.0.
Scott
On Thu, Mar 19, 2009 at 8:52 AM, Scott Cain <scott at scottcain.net> wrote:
> 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
>
--
------------------------------------------------------------------------
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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