[Gmod-help] problems with Gbrowse 1.69
Scott Cain
cain.cshl at gmail.com
Tue Oct 7 15:48:07 EDT 2008
Hi Jason,
I agree that something strange is happening at about the point when
it's trying to draw the overview, but I don't know what that something
is. When I tried to look at the yeast database to see if it was
working, it looked like the attached picture. Note that the images
for the zoom and pan buttons are missing. I think there is a
misconfiguration somewhere. Where any directories moved or apache
configuration file changes made?
Scott
On Tue, Oct 7, 2008 at 3:28 PM, Jason Phillips <japhill at email.unc.edu> wrote:
> Scott,
> That's true. Gbrowse 1.69 was working fine and it just seemed to to stop. I
> talked with the system's administrator of the server, and he said that
> nothing had change at least on the bio perl front. I am not aware of
> another gbrowse installation, though I could talk to him and ask about that
> too.
>
> One thing that I know changed is that we installed an ssl certificate in a
> directory not related to the gbrowse directory. But I can tyep the url to
> the gbrowser using https and it works and breaks the same as typing http.
>
> The problems started showing up in the logs a few days before the ssl
> certificate installation was finished so I'm not too sure if that is related
> to the problem.
>
> You can try typing this into your browser to see how much does show. It
> seems like it dies when trying to display the actual overview feature
> graphic.
> https://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_7x/
>
>
> Thanks
>
> Jason
>
> On Tue, 7 Oct 2008, Scott Cain wrote:
>
>> 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
>>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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