[Gmod-help] problems with Gbrowse 1.69

[Scott Cain]

Hi Jason,

I'm sorry--Bio::Graphics::Browser is provided by GBrowse.  Have you
installed GBrowse in more than one location on the server?

Also, you said that it just stopped working.  I assume from that
statement that at some point recently, GBrowse 1.69 was working,
correct?

Scott

On Tue, Oct 7, 2008 at 2:57 PM, Jason Phillips <japhill at email.unc.edu> wrote:
> Scott,
> I could only find one occurance of the installation.  I attached the
> Graphics::Browser file that is on our server.  I don't have permissions
> right now to due too much on the server but can look at the files at least.
>  Is the file I attached indeed from the bioperl live?
>
>
> Thanks a million!
>
> Jason
>
>
>  On Tue, 7 Oct 2008, Scott Cain wrote:
>
>> Hi Jason,
>>
>> The "can't locate method" message makes me wonder if there is more
>> than one bioperl installed on the server, and so it's not using the
>> right Bio::Graphics::Browser.  Is that a possibility?
>>
>> Scott
>>
>>
>> On Tue, Oct 7, 2008 at 1:57 PM, Jason Phillips <japhill at email.unc.edu>
>> wrote:
>>>
>>> I'm beating my head against this problem that seems to have spontaneously
>>> appeared in my gbrowse configuration.  We are using 1.69 and have updated
>>> the bioperl to use the 'live' version straight from cvs.  It seemed like
>>> over night the browser stopped working correctly.  I looked in my httpd
>>> log
>>> and found these associated with requesting gbrowse data from firefox:
>>>
>>> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224]
>>> Bio::Graphics::BrowserConfig=HASH(0x3fcc050) at
>>>
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>> line 587., referer:
>>> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
>>> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224]
>>> Bio::Graphics::BrowserConfig=HASH(0x3fcc050) at
>>>
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>> line 587., referer:
>>> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
>>> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224] Use of
>>> uninitialized value in numeric gt (>) at
>>>
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/UploadSet.pm
>>> line 155., referer:
>>> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
>>> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224] Can't locate
>>> object method "overview" via package "Bio::Graphics::Browser" at
>>> /home/www/cgi-bin/gbrowse line 1925., referer:
>>> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
>>>
>>>
>>> Can you narrow down the possible problems that these log entries would
>>> indicate?
>>>
>>> Let me know if you need more information to diagnose the problem.
>>>
>>>
>>> Thanks
>>>
>>> Jason Phillips
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   cain.cshl at gmail.com
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research