establishing chado connections
Locked
establishing chado connections
 
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I’m attempting to connect to Chado with Gbrowse 2.49.
My Gbrowse conf is at its defaults when installed with these edits: [GENERAL] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado; config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse
############################################################################################### # # DATASOURCE DEFINITIONS # One stanza for each configured data source # ###############################################################################################
[chado] description = Chado Database path = Chado.conf
My chado conf is: [GENERAL] description = Chado database database = chado
initial landmark = chrI:143000..180000 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1
default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region
# examples to show in the introduction examples = chrI chrII chrI:80,000..120,000 "membrane trafficking" NUT21 YAL063C
# "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone
################################# # database definitions #################################
[chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo
When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser, and my apache error log shows:
[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse
I appreciate any advice or help that can be given to solve this problem.
David Jeang This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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Update: after getting GCI::Toggle to work, the error log now states: [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8 .) at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1240. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1270. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 404. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 357. [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin) [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico The browser says
I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for. But the tripal database is on a
PostgreSQL 8.4.12 server running on
localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site
http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files? David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
I’m attempting to connect to Chado with Gbrowse 2.49. My Gbrowse conf is at its defaults when installed with these edits: [GENERAL] db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado;
config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse ############################################################################################### # # DATASOURCE DEFINITIONS # One stanza for each configured data source # ############################################################################################### [chado] description = Chado Database path = Chado.conf My chado conf is: [GENERAL] description = Chado database database = chado initial landmark = chrI:143000..180000 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1 default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region # examples to show in the introduction examples = chrI chrII chrI:80,000..120,000 "membrane trafficking" NUT21 YAL063C # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ################################# # database definitions ################################# [chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,
and my apache error log shows: [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse I appreciate any advice or help that can be given to solve this problem. David Jeang
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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I’ve managed to adjust some permissions that clear up the DBD::Pg problem, now I have this error in the log: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] DBD::Pg::st execute failed: ERROR: relation "cv" does not exist [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] LINE 1: select cv_id from cv where name in ( [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ^ at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das/ Chado.pm line 843. [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] Could not open database: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ------------- EXCEPTION: Bio::Root::Exception ------------- [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] MSG: trying to find SOFA [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Error::throw [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::sofa_id /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB /Das/Chado.pm:843 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::new /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das /Chado.pm:242 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux -thread-multi/Bio/Graphics/Browser2/DataBase.pm:44 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-lin ux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:981 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-t hread-multi/Bio/Graphics/Browser2/Render.pm:1084 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul ti/Bio/Graphics/Browser2/Render.pm:343 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::run /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult i/Bio/Graphics/Browser2/Render.pm:285 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: /var/www/cgi-bin/gb2/gbrowse:50 Can anyone tell me what is means? David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
Update: after getting GCI::Toggle to work, the error log now states: [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8 .) at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1240. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1270. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 404. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 357. [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin) [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico The browser says
I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for. But the tripal database is on a
PostgreSQL 8.4.12 server running on
localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site
http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files? David Jeang From: Jeang, David - ARS [[hidden email]]
I’m attempting to connect to Chado with Gbrowse 2.49. My Gbrowse conf is at its defaults when installed with these edits: [GENERAL] db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado;
config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse ############################################################################################### # # DATASOURCE DEFINITIONS # One stanza for each configured data source # ############################################################################################### [chado] description = Chado Database path = Chado.conf My chado conf is: [GENERAL] description = Chado database database = chado initial landmark = chrI:143000..180000 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1 default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region # examples to show in the introduction examples = chrI chrII chrI:80,000..120,000 "membrane trafficking" NUT21 YAL063C # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ################################# # database definitions ################################# [chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,
and my apache error log shows: [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse I appreciate any advice or help that can be given to solve this problem. David Jeang
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
|
|
Is…anyone even listening to my problems anymore? Because I’m a little pressed for time, I have about 2 weeks to get this set up, if that’s alright with you. David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
I’ve managed to adjust some permissions that clear up the DBD::Pg problem, now I have this error in the log: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] DBD::Pg::st execute failed: ERROR: relation "cv" does not exist [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] LINE 1: select cv_id from cv where name in ( [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ^ at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das/ Chado.pm line 843. [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] Could not open database: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ------------- EXCEPTION: Bio::Root::Exception ------------- [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] MSG: trying to find SOFA [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Error::throw [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::sofa_id /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB /Das/Chado.pm:843 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::new /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das /Chado.pm:242 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux -thread-multi/Bio/Graphics/Browser2/DataBase.pm:44 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-lin ux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:981 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-t hread-multi/Bio/Graphics/Browser2/Render.pm:1084 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul ti/Bio/Graphics/Browser2/Render.pm:343 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::run /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult i/Bio/Graphics/Browser2/Render.pm:285 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: /var/www/cgi-bin/gb2/gbrowse:50 Can anyone tell me what is means? David Jeang From: Jeang, David - ARS [[hidden email]]
Update: after getting GCI::Toggle to work, the error log now states: [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8 .) at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1240. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1270. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 404. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 357. [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin) [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224. [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico The browser says
I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for. But the tripal database is on a
PostgreSQL 8.4.12 server running on
localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site
http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files? David Jeang From: Jeang, David - ARS [[hidden email]]
I’m attempting to connect to Chado with Gbrowse 2.49. My Gbrowse conf is at its defaults when installed with these edits: [GENERAL] db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado;
config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse ############################################################################################### # # DATASOURCE DEFINITIONS # One stanza for each configured data source # ############################################################################################### [chado] description = Chado Database path = Chado.conf My chado conf is: [GENERAL] description = Chado database database = chado initial landmark = chrI:143000..180000 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1 default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region # examples to show in the introduction examples = chrI chrII chrI:80,000..120,000 "membrane trafficking" NUT21 YAL063C # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ################################# # database definitions ################################# [chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,
and my apache error log shows: [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse I appreciate any advice or help that can be given to solve this problem. David Jeang
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
|
In reply to this post by Jeang, David - ARS
Hi David,
Sorry about the radio silence; I've been traveling a lot the last few weeks so a few things have slipped. I'd say the fact that it is complaining about not finding the cv table means two things: 1. It is successfully connecting to the database (that's a good thing), and 2. You don't have the search path set appropriately for the user that's connecting to the database. Since you're using GBrowse with Tripal, you have to set the search path for the user that is connecting so that it searches the chado schema first. Scott On Fri, Jul 20, 2012 at 2:58 PM, Jeang, David - ARS <[hidden email]> wrote:
-- ------------------------------------------------------------------------ Scott Cain, Ph. D.                  scott at scottcain dot net GMOD Coordinator (http://gmod.org/)           216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
|
|
Thank you. I can understand that. [chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado; <- This line I put here in both the Gbrowse and Chado conf should get it to look through chado first right? Also, the server the postgres database is on is port 5432 for localhost, is that information needed? David Jeang From: Scott Cain [mailto:[hidden email]]
Hi David, On Fri, Jul 20, 2012 at 2:58 PM, Jeang, David - ARS <[hidden email]> wrote: I’ve managed to adjust some permissions that clear up the DBD::Pg problem, now I have this error in the log: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] DBD::Pg::st execute failed: ERROR: relation "cv" does not exist [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] LINE 1: select cv_id from cv where name in ( [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ^ at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das/ Chado.pm line 843. [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] Could not open database: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ------------- EXCEPTION: Bio::Root::Exception ------------- [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] MSG: trying to find SOFA [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Error::throw [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::sofa_id /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB /Das/Chado.pm:843 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::new /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das /Chado.pm:242 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux -thread-multi/Bio/Graphics/Browser2/DataBase.pm:44 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-lin ux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:981 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-t hread-multi/Bio/Graphics/Browser2/Render.pm:1084 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul ti/Bio/Graphics/Browser2/Render.pm:343 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::run /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult i/Bio/Graphics/Browser2/Render.pm:285 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: /var/www/cgi-bin/gb2/gbrowse:50 Can anyone tell me what is means? David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
Update: after getting GCI::Toggle to work, the error log now states: [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg
in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8
/usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm
line 1240. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm
line 1270. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 404. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm
line 357. [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin) [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico The browser says
I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for.
But the tripal database is on a PostgreSQL 8.4.12 server running on localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site
http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files? David Jeang From: Jeang, David - ARS [[hidden email]]
I’m attempting to connect to Chado with Gbrowse 2.49. My Gbrowse conf is at its defaults when installed with these edits:
[GENERAL]
db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado
-dsn dbi:Pg:dbname=tripal;host=localhost
-user tripaldemo
-pass tripal2demo
psql= ALTER USER tripaldemo SET search_path TO chado;
config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF
htdocs_base = /var/www/html/gbrowse2
url_base = /gbrowse2
tmp_base = /var/tmp/gbrowse2
persistent_base = /var/lib/gbrowse2
userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse
###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################
[chado]
description = Chado Database path = Chado.conf My chado conf is:
[GENERAL]
description = Chado database
database = chado
initial landmark = chrI:143000..180000
plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper
autocomplete = 1
default tracks = Genes
ORFs
tRNAs
CDS
Transp
Centro:overview
GC:region
# examples to show in the introduction
examples = chrI
chrII
chrI:80,000..120,000
"membrane trafficking"
NUT21
YAL063C
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[chado:database]
db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado
-dsn dbi:Pg:dbname=tripal;host=localhost
-user tripaldemo -pass tripal2demo When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,
and my apache error log shows: [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse I appreciate any advice or help that can be given to solve this problem. David Jeang
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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Nevermind, I figured it out. The postgre server did not grant permissions for tripaldemo to select the cv, I altered it so that it could. Problem solved! David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
Thank you. I can understand that. [chado:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql= ALTER USER tripaldemo SET search_path TO chado; <- This line I put here in both the Gbrowse and Chado conf should get it to look through chado first right? Also, the server the postgres database is on is port 5432 for localhost, is that information needed? David Jeang From: Scott Cain [[hidden email]]
Hi David, On Fri, Jul 20, 2012 at 2:58 PM, Jeang, David - ARS <[hidden email]> wrote: I’ve managed to adjust some permissions that clear up the DBD::Pg problem, now I have this error in the log: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] DBD::Pg::st execute failed: ERROR: relation "cv" does not exist [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] LINE 1: select cv_id from cv where name in ( [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ^ at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das/ Chado.pm line 843. [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] Could not open database: [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ------------- EXCEPTION: Bio::Root::Exception ------------- [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] MSG: trying to find SOFA [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Error::throw [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::sofa_id /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB /Das/Chado.pm:843 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::new /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das /Chado.pm:242 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux -thread-multi/Bio/Graphics/Browser2/DataBase.pm:44 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-lin ux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:981 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-t hread-multi/Bio/Graphics/Browser2/Render.pm:1084 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul ti/Bio/Graphics/Browser2/Render.pm:343 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::run /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult i/Bio/Graphics/Browser2/Render.pm:285 [Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: /var/www/cgi-bin/gb2/gbrowse:50 Can anyone tell me what is means? David Jeang From: Jeang, David - ARS [mailto:[hidden email]]
Update: after getting GCI::Toggle to work, the error log now states: [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg
in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8
/usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm
line 1240. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm
line 1270. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 131. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 141. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm
line 1048. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm
line 404. [Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm
line 357. [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin) [Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm
line 224. [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico The browser says
I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for.
But the tripal database is on a PostgreSQL 8.4.12 server running on localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site
http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files? David Jeang From: Jeang, David - ARS [[hidden email]]
I’m attempting to connect to Chado with Gbrowse 2.49. My Gbrowse conf is at its defaults when installed with these edits:
[GENERAL]
db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado
-dsn dbi:Pg:dbname=tripal;host=localhost
-user tripaldemo
-pass tripal2demo
psql= ALTER USER tripaldemo SET search_path TO chado;
config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF
htdocs_base = /var/www/html/gbrowse2
url_base = /gbrowse2
tmp_base = /var/tmp/gbrowse2
persistent_base = /var/lib/gbrowse2
userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse
###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################
[chado]
description = Chado Database path = Chado.conf My chado conf is:
[GENERAL]
description = Chado database
database = chado
initial landmark = chrI:143000..180000
plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper
autocomplete = 1
default tracks = Genes
ORFs
tRNAs
CDS
Transp
Centro:overview
GC:region
# examples to show in the introduction
examples = chrI
chrII
chrI:80,000..120,000
"membrane trafficking"
NUT21
YAL063C
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
#################################
# database definitions
#################################
[chado:database]
db_adaptor = Bio::DB::Das::Chado
db_args = -adaptor Bio::DB::Das::Chado
-dsn dbi:Pg:dbname=tripal;host=localhost
-user tripaldemo -pass tripal2demo When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,
and my apache error log shows: [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
line 64, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192. [Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse I appreciate any advice or help that can be given to solve this problem. David Jeang
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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In reply to this post by Jeang, David - ARS
Hi David,
I agree that using ALTER USER should do the trick. What happens when you use the psql shell on the command line as that user? You could try a simple query like SELECT count(*) FROM cv; to see if it finds the cv table. If that appears to work, we should ask on the tripal mailing list, since they more experience with this sort of thing. Scott On Thu, Jul 26, 2012 at 10:31 AM, Jeang, David - ARS <[hidden email]> wrote:
-- ------------------------------------------------------------------------ Scott Cain, Ph. D.                  scott at scottcain dot net GMOD Coordinator (http://gmod.org/)           216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
|
In reply to this post by Jeang, David - ARS
Hi Scott/David, It's been a while ago, but for what it's worth, when I set up GBrowse + Chado, cv was one of the tables (perhaps the only table) which didn't have permissions granted to it. I had to grant the permissions manually. I never investigated what the reason was, though. Ray On Thursday, July 26, 2012 11:49 PM, Scott Cain wrote:> Hi David, > > I agree that using ALTER USER should do the trick. What > happens when you use the psql shell on the command line as > that user? You could try a simple query like SELECT > count(*) FROM cv; to see if it finds the cv table. If that > appears to work, we should ask on the tripal mailing list, > since they more experience with this sort of thing. > > Scott ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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|
Hi Ray,
Thanks, though in this case I don't think that is the problem. The error message was that it couldn't find cv, not that it had a permission problem. Scott On Fri, Jul 27, 2012 at 1:32 PM, Raymond Wan <[hidden email]> wrote: > > Hi Scott/David, > > It's been a while ago, but for what it's worth, when I set up GBrowse + Chado, > cv was one of the tables (perhaps the only table) which didn't have permissions > granted to it. I had to grant the permissions manually. I never investigated > what the reason was, though. > > Ray > > > On Thursday, July 26, 2012 11:49 PM, Scott Cain wrote:> Hi David, >> >> I agree that using ALTER USER should do the trick. What >> happens when you use the psql shell on the command line as >> that user? You could try a simple query like SELECT >> count(*) FROM cv; to see if it finds the cv table. If that >> appears to work, we should ask on the tripal mailing list, >> since they more experience with this sort of thing. >> >> Scott > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
|
|
Scott, I said before it WAS a permission problem and it was solved... David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Friday, July 27, 2012 2:28 PM To: Raymond Wan Cc: Jeang, David - ARS; [hidden email] Subject: Re: [Gmod-gbrowse] establishing chado connections Hi Ray, Thanks, though in this case I don't think that is the problem. The error message was that it couldn't find cv, not that it had a permission problem. Scott On Fri, Jul 27, 2012 at 1:32 PM, Raymond Wan <[hidden email]> wrote: > > Hi Scott/David, > > It's been a while ago, but for what it's worth, when I set up GBrowse > + Chado, cv was one of the tables (perhaps the only table) which > didn't have permissions granted to it. I had to grant the permissions > manually. I never investigated what the reason was, though. > > Ray > > > On Thursday, July 26, 2012 11:49 PM, Scott Cain wrote:> Hi David, >> >> I agree that using ALTER USER should do the trick. What happens when >> you use the psql shell on the command line as that user? You could >> try a simple query like SELECT >> count(*) FROM cv; to see if it finds the cv table. If that appears >> to work, we should ask on the tripal mailing list, since they more >> experience with this sort of thing. >> >> Scott > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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|
Oh <blush> forgot that you wrote that. Thanks for pointing it out.
Scott On Fri, Jul 27, 2012 at 4:01 PM, Jeang, David - ARS <[hidden email]> wrote: > > Scott, I said before it WAS a permission problem and it was solved... > > David Jeang > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Friday, July 27, 2012 2:28 PM > To: Raymond Wan > Cc: Jeang, David - ARS; [hidden email] > Subject: Re: [Gmod-gbrowse] establishing chado connections > > Hi Ray, > > Thanks, though in this case I don't think that is the problem. The error message was that it couldn't find cv, not that it had a permission problem. > > Scott > > > On Fri, Jul 27, 2012 at 1:32 PM, Raymond Wan <[hidden email]> wrote: >> >> Hi Scott/David, >> >> It's been a while ago, but for what it's worth, when I set up GBrowse >> + Chado, cv was one of the tables (perhaps the only table) which >> didn't have permissions granted to it. I had to grant the permissions >> manually. I never investigated what the reason was, though. >> >> Ray >> >> >> On Thursday, July 26, 2012 11:49 PM, Scott Cain wrote:> Hi David, >>> >>> I agree that using ALTER USER should do the trick. What happens when >>> you use the psql shell on the command line as that user? You could >>> try a simple query like SELECT >>> count(*) FROM cv; to see if it finds the cv table. If that appears >>> to work, we should ask on the tripal mailing list, since they more >>> experience with this sort of thing. >>> >>> Scott >> >> >> ------------------------------------------------- >> This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
Hi,
May I know is it the chado is another option for mysql database? If yes, which one better? i have upload the seq into mysql but it doesnt appear when i click the gene.... thank you On Sat, Jul 28, 2012 at 4:13 AM, Scott Cain <[hidden email]> wrote: Oh <blush> forgot that you wrote that. Â Thanks for pointing it out. -- Shuhaila Binti Mat Sharani BSc (Hons) Bioinformatics Graduate Student Universiti Kebangsaan Malaysia 43600 Bangi Selangor, Malaysia. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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Hi, Quoting shu ms <[hidden email]>: > May I know is it the chado is another option for mysql database? > > If yes, which one better? Chado is a database schema; MySQL is a DBMS (database management system). A database schema specifies how the data is stored (what tables are there and how the tables relate to each other). A DBMS such as MySQL is a program that creates tables (etc.) according to a schema for storing data. So, they aren't the same and, actually, work together. You can replace MySQL with another DBMS such as PostgreSQL. You can also replace Chado with something else (though I have never tried). I don't know if this is up to date, but this gives a summary of your choices: http://gmod.org/wiki/GBrowse#About_Databases IMHO, getting Chado to work is a bit complex. But if you are using something else and the "con" in that table bothers you, then it might be worth trying another option such as Chado. If you're new to GBrowse, I'd pick the option with the most help documentation and when you've got it figured out, then try the options you would have wanted to try. :-) > i have upload the seq into mysql but it doesnt appear when i click the > gene.... That sounds like a problem with something else such as how GBrowse is connected to your database. If you can load sequences fine but are unable to click on genes, it is possible you haven't loaded the gene annotations yet? Ray ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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Hi Ray and Shuhaila,
Ray, thanks for the excellent summary. I would agree that Chado would not be the first choice when using GBrowse unless you had a good reason to be using Chado for other things as well. Additionally, we don't support Chado with MySQL. Finally, I agree with Ray that the problem associated with upload difficulties is almost certainly not related to what database schema you are using; it is more likely a problem related to file and directory permissions, or something misconfigured in the GBrowse conf file. Scott On 7/28/12, Raymond Wan <[hidden email]> wrote: > > Hi, > > > Quoting shu ms <[hidden email]>: > >> May I know is it the chado is another option for mysql database? >> >> If yes, which one better? > > > Chado is a database schema; MySQL is a DBMS (database management system). > A > database schema specifies how the data is stored (what tables are there and > how > the tables relate to each other). A DBMS such as MySQL is a program that > creates tables (etc.) according to a schema for storing data. > > So, they aren't the same and, actually, work together. You can replace > MySQL > with another DBMS such as PostgreSQL. You can also replace Chado with > something else (though I have never tried). > > I don't know if this is up to date, but this gives a summary of your > choices: > > http://gmod.org/wiki/GBrowse#About_Databases > > IMHO, getting Chado to work is a bit complex. But if you are using > something > else and the "con" in that table bothers you, then it might be worth trying > another option such as Chado. > > If you're new to GBrowse, I'd pick the option with the most help > documentation > and when you've got it figured out, then try the options you would have > wanted > to try. :-) > > >> i have upload the seq into mysql but it doesnt appear when i click the >> gene.... > > > That sounds like a problem with something else such as how GBrowse is > connected > to your database. If you can load sequences fine but are unable to click > on > genes, it is possible you haven't loaded the gene annotations yet? > > Ray > > > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Gmod-gbrowse mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections
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Hi Scott, Quoting Scott Cain <[hidden email]>: > Ray, thanks for the excellent summary. I would agree that Chado would > not be the first choice when using GBrowse unless you had a good > reason to be using Chado for other things as well. Additionally, we > don't support Chado with MySQL. Finally, I agree with Ray that the Thanks! Actually, I didn't know that Chado didn't work with MySQL. I used PostgreSQL with Chado and I thought my choice was 'arbitrary'. Thanks for mentioning this explicitly or else I wouldn't have known/noticed! Ray ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
establishing chado connections: Working out the tracks in conf
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In reply to this post by Scott Cain
My Gbrowse is now officially connected to the chado database, extracting the data with conf tracks is taking a little effort to get through.
I've started off with a simple track: [CG12567] feature = mRNA glyph = span height = 5 description = 1 key = CG12567 After finally removing all permission problems from the database and its functions, I'm now left with a blank browser and the error log says: [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Use of uninitialized value in subtraction (-) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 2025., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Can't locate object method "score" via package "Bio::DB::Das::Chado::Segment" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Karyotype.pm line 362., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] 11 12 13 76, referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 385., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 314., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 167., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ I'm a little stumped on where to go from here. Any suggestions? David Jeang This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections: Working out the tracks in conf
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Hi David,
Many times the "uninit in a subtraction" is due to not having a properly defined reference sequence. What does the GFF look like that defines the chromosome and the mRNA features? Scott On Wed, Aug 1, 2012 at 3:55 PM, Jeang, David - ARS <[hidden email]> wrote: > My Gbrowse is now officially connected to the chado database, extracting the data with conf tracks is taking a little effort to get through. > > I've started off with a simple track: > > [CG12567] > feature = mRNA > glyph = span > height = 5 > description = 1 > key = CG12567 > > After finally removing all permission problems from the database and its functions, I'm now left with a blank browser and the error log says: > > [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Use of uninitialized value in subtraction (-) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 2025., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Can't locate object method "score" via package "Bio::DB::Das::Chado::Segment" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Karyotype.pm line 362., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] 11 12 13 76, referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 385., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 314., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of uninitialized value in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 167., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > > > I'm a little stumped on where to go from here. Any suggestions? > > David Jeang > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections: Working out the tracks in conf
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How would I go about finding the gffs? In my schema, I have tables, views, sequences, and functions.
Is there a SQL command I can use on the tripal database? David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Wednesday, August 01, 2012 4:48 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: establishing chado connections: Working out the tracks in conf Hi David, Many times the "uninit in a subtraction" is due to not having a properly defined reference sequence. What does the GFF look like that defines the chromosome and the mRNA features? Scott On Wed, Aug 1, 2012 at 3:55 PM, Jeang, David - ARS <[hidden email]> wrote: > My Gbrowse is now officially connected to the chado database, extracting the data with conf tracks is taking a little effort to get through. > > I've started off with a simple track: > > [CG12567] > feature = mRNA > glyph = span > height = 5 > description = 1 > key = CG12567 > > After finally removing all permission problems from the database and its functions, I'm now left with a blank browser and the error log says: > > [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Use of > uninitialized value in subtraction (-) at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic > s/Browser2/Render/HTML.pm line 2025., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Can't locate > object method "score" via package "Bio::DB::Das::Chado::Segment" at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic > s/Karyotype.pm line 362., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] 11 12 13 76, > referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of > uninitialized value in join or string at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic > s/Browser2/Region.pm line 385., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of > uninitialized value in join or string at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic > s/Browser2/RegionSearch.pm line 314., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of > uninitialized value in join or string at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic > s/Browser2/Region.pm line 167., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ > > > I'm a little stumped on where to go from here. Any suggestions? > > David Jeang > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: establishing chado connections: Working out the tracks in conf
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Hi David,
How did you originally load the database? The typical way is to use GFF and a loader, either the one that comes with Tripal or the one that comes with Chado. Scott On Thu, Aug 2, 2012 at 11:44 AM, Jeang, David - ARS <[hidden email]> wrote: > How would I go about finding the gffs? In my schema, I have tables, views, sequences, and functions. > > Is there a SQL command I can use on the tripal database? > > David Jeang > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, August 01, 2012 4:48 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: establishing chado connections: Working out the tracks in conf > > Hi David, > > Many times the "uninit in a subtraction" is due to not having a properly defined reference sequence. What does the GFF look like that defines the chromosome and the mRNA features? > > Scott > > > On Wed, Aug 1, 2012 at 3:55 PM, Jeang, David - ARS <[hidden email]> wrote: >> My Gbrowse is now officially connected to the chado database, extracting the data with conf tracks is taking a little effort to get through. >> >> I've started off with a simple track: >> >> [CG12567] >> feature = mRNA >> glyph = span >> height = 5 >> description = 1 >> key = CG12567 >> >> After finally removing all permission problems from the database and its functions, I'm now left with a blank browser and the error log says: >> >> [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Use of >> uninitialized value in subtraction (-) at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic >> s/Browser2/Render/HTML.pm line 2025., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:01:53 2012] [error] [client 10.12.20.67] Can't locate >> object method "score" via package "Bio::DB::Das::Chado::Segment" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic >> s/Karyotype.pm line 362., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] 11 12 13 76, >> referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of >> uninitialized value in join or string at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic >> s/Browser2/Region.pm line 385., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of >> uninitialized value in join or string at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic >> s/Browser2/RegionSearch.pm line 314., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> [Wed Aug 01 12:02:34 2012] [error] [client 10.12.20.67] Use of >> uninitialized value in join or string at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic >> s/Browser2/Region.pm line 167., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/ >> >> >> I'm a little stumped on where to go from here. Any suggestions? >> >> David Jeang >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> > > > > -- > ------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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