vista_plot glyph fails to load

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vista_plot glyph fails to load

John Portwood
Hello,

On 10/02/14 I installed the CPAN version of GBrowse (2.56?)  and BioGraphics
(2.38?) on a server running CentOS 6.5. We have a separate instance of
GBrowse (2.43) in a production environment already, but we are upgrading to
new hardware and so my task is replicate our production instance as close as
possible on the new machine. All of the migrated tracks are working fine,
except for one that uses the "vista_plot" glyph. This track works on the
2.43 instance of GBrowse, but on the 2.56 instance this error is generated:

RUN(): POST: http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false
at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.,
referer: http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:18 2014] [error] [client 129.186.136.159] [6854] session
id = 57fa6dc06726b4f9543ef28482ec62cf at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244., referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:18 2014] [error] [client 129.186.136.159] [6854]
add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm
line 273., referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:18 2014] [error] [client 129.186.136.159] [6854] testing
for asynchronous event() at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276., referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: [6854] asynchronous exit at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 278., referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: RenderPanels error: , referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: ------------- EXCEPTION: Bio::Root::Exception
-------------, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: MSG: The requested glyph class, ``vista_plot'' is
not available: Attempt to reload Bio/Graphics/Glyph/vista_plot.pm aborted.,
referer: http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: Compilation failed in require at (eval 391) line 3.,
referer: http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: , referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Error::throw, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Root::Root::throw
/usr/local/share/perl5/Bio/Root/Root.pm:472, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::Factory::make_glyph
/usr/local/share/perl5/Bio/Graphics/Glyph/Factory.pm:342, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::make_subglyph
/usr/local/share/perl5/Bio/Graphics/Glyph.pm:310, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::new
/usr/local/share/perl5/Bio/Graphics/Glyph.pm:270, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::group::new
/usr/local/share/perl5/Bio/Graphics/Glyph/group.pm:93, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::Factory::make_glyph
/usr/local/share/perl5/Bio/Graphics/Glyph/Factory.pm:346, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Glyph::add_feature
/usr/local/share/perl5/Bio/Graphics/Glyph.pm:423, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::RenderPanels::add_features_to_track
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1889, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::RenderPanels::run_local_requests
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1581, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::RenderPanels::request_panels
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:189, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::Render::render_deferred
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:3587, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::Render::background_track_render
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:498, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::Action::ACTION_navigate
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Action.pm:141, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::Render::asynchronous_event
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:430, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK:
Bio::Graphics::Browser2::Render::run_asynchronous_event
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:359, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: Bio::Graphics::Browser2::Render::run
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:277, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse: STACK: /var/www/cgi-bin/gb2/gbrowse:54, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/
[Tue Oct 07 11:36:19 2014] [error] [client 129.186.136.159] [Tue Oct  7
11:36:19 2014] gbrowse:
-----------------------------------------------------------, referer:
http://gblade.gdcb.iastate.edu/cgi-bin/gb2/gbrowse/maize_v2/

I've ensured the latest BioGraphics is installed and that vista_plot.pm
exists in the correct directory. This track is using the exact same data and
configuration on both GBrowse instances I have set up, so I think there's a
problem with my recent installation.

Here's a snippet of the GFF3 file:
Chr1    Hakes   MAC     4241    301348330       .       .       .      
Name=KN1_Ear1;subtrack=0;wigfile=/var/www/html/gbrowse/databases/kn1/kn1_wibfiles/track_001.Chr1.1350328517.wib;peak_type=MAC_Overlap:Hakes
Chr10   Hakes   MAC     2841    150184180       .       .       .      
Name=KN1_Ear1;subtrack=0;wigfile=/var/www/html/gbrowse/databases/kn1/kn1_wibfiles/track_001.Chr10.1350328571.wib;peak_type=MAC_Overlap:Hakes
Chr2    Hakes   MAC     9001    237067170       .       .       .      
Name=KN1_Ear1;subtrack=0;wigfile=/var/www/html/gbrowse/databases/kn1/kn1_wibfiles/track_001.Chr2.1350328613.wib;peak_type=MAC_Overlap:Hakes
Chr3    Hakes   MAC     551     232136290       .       .       .      
Name=KN1_Ear1;subtrack=0;wigfile=/var/www/html/gbrowse/databases/kn1/kn1_wibfiles/track_001.Chr3.1350328667.wib;peak_type=MAC_Overlap:Hakes
Chr4    Hakes   MAC     1221    241467300       .       .       .      
Name=KN1_Ear1;subtrack=0;wigfile=/var/www/html/gbrowse/databases/kn1/kn1_wibfiles/track_001.Chr4.1350328721.wib;peak_type=MAC_Overlap:Hakes

The path in the wigfile parameter exists and apache has ownership of it. Any
help on pinpointing the cause of the issue would be much-appreciated.

Thanks!



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Re: vista_plot glyph fails to load

John Portwood
I've resolved the issue now. Turns out I did not have Bio::DB::BigFile
properly installed. Compiling the vista_plot file individually with "perl -c
vista_plot.pm" spat out a more informative error.

Thanks!



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