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rayapadi swetha
Dear,

I am new bie to GBrowse. I installed Gbrowse in my system and learning how to use it from the tutorial. I stuck at 1.5 Adding descriptions to a feature in tutorial. I followed the instructions given in the tutorial.

1. copied volvox_domains.gff3 in /var/lib/gbrowse2/databases/volvox directory

2. pasted in volvox.conf file
[Motifs]
feature      = polypeptide_domain
glyph        = span
height       = 5
description  = 1
key          = Example motifs

when I run, it throws error. 

[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::RegionSearch::init_databases /usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm:125, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::get_search_object /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1234, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::PluginSet::configure /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm:88, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::init_plugins /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1279, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Action::ACTION_retrieve_multiple /usr/local/lib64/perl5/Bio/Graphics/Browser2/Action.pm:282, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::asynchronous_event /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:430, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::run_asynchronous_event /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:359, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:277, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: /var/apache/cgi-bin/gb2/gbrowse:54, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] -----------------------------------------------------------, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/


Can you please assist with this error. Thank you so much. waiting for your reply.

regards,
Swetha Rayapadi


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Re: Help

Scott Cain
Hi Swetha,

I don't think that's the beginning of the error message; can you please get more of it from the error log?

Scott


Sent from my iPad

On Apr 25, 2014, at 12:12 AM, rayapadi swetha <[hidden email]> wrote:

Dear,

I am new bie to GBrowse. I installed Gbrowse in my system and learning how to use it from the tutorial. I stuck at 1.5 Adding descriptions to a feature in tutorial. I followed the instructions given in the tutorial.

1. copied volvox_domains.gff3 in /var/lib/gbrowse2/databases/volvox directory

2. pasted in volvox.conf file
[Motifs]
feature      = polypeptide_domain
glyph        = span
height       = 5
description  = 1
key          = Example motifs

when I run, it throws error. 

[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::RegionSearch::init_databases /usr/local/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm:125, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::get_search_object /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1234, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::PluginSet::configure /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm:88, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::init_plugins /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1279, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Action::ACTION_retrieve_multiple /usr/local/lib64/perl5/Bio/Graphics/Browser2/Action.pm:282, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::asynchronous_event /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:430, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::run_asynchronous_event /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:359, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:277, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] STACK: /var/apache/cgi-bin/gb2/gbrowse:54, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/
[Fri Apr 25 09:14:34 2014] [error] [client 10.132.1.14] -----------------------------------------------------------, referer: http://10.132.1.14/cgi-bin/gb2/gbrowse/volvox/


Can you please assist with this error. Thank you so much. waiting for your reply.

regards,
Swetha Rayapadi

------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
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------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
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