[Gmod-help] problems with Gbrowse 1.69
Dave Clements, GMOD Help Desk
gmodhelp at googlemail.com
Tue Oct 7 16:20:40 EDT 2008
Jason, Scott,
Sorry, I was researching something else for the past two hours.
Well, danged if I know what is going on either. However, the given
server is at NESCent and I can probably get the same access to it that
Jason has. I'll see what I can do.
In the meantime, if either of you two has new insights please do
share. It may take me a while to get access.
Thanks,
Dave C.
On Tue, Oct 7, 2008 at 12:48 PM, Scott Cain <cain.cshl at gmail.com> wrote:
> 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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