Re: help regarding gbrowse

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

Please always ask questions like this on the GBrowse mailing list (cc'ed here).

Do you have apache installed and running?  What is in the apache error log (probably in /var/log/apache2/error_log)?

Scott



On Tue, Aug 12, 2014 at 1:45 AM, umay kulsum <[hidden email]> wrote:
hello Scott,

I have installed gbrowse2 via CPAN shell using the command in ubuntu 14.04:

sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'

but the example file of yeast not working with the url
http://localhost/gbrowse2/yeast
it shows the error the rquested url was not found on this server.

all the files are installed at default locations such as:
/usr/lib/cgi-bin/gb2/gbrowse
/etc/gbrowse2/GBrowse.conf

but nothing is found in /var/tmp/gbrowse2

Can you please help in solving this.

Regards

Umay Kulsum
PhD Student
AIIMS



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: help regarding gbrowse

Scott Cain
Hi Umay,

The email address is [hidden email], and you get a moderation message because you have to be subscribed to the list in order to send messages to it without moderation.  I have always allowed your messages onto the list; the moderation is to keep spammers out.

A few things:

1. The url you are trying (http://localhost/gbrowse2/yeast) won't get you a GBrowse page unless you've done something unusual with your apache config.  A more typical URL would be http://localhost/cgi-bin/gb2/gbrowse/yeast

2. What OS are you using? The apache error log segment makes me think Centos or Fedora but the path to the cgi you originally posted makes me think Debian or Ubuntu. 

3. While you weren't using the correct URL to access GBrowse, the file permissions error in the error log has me worried that something went wrong during the installation, as it should set the permissions correctly.  Do you recall any messages about problems during the installation?

Scott



On Thu, Aug 14, 2014 at 12:02 AM, umay kulsum <[hidden email]> wrote:
Dear Scott
when I mail my question to [hidden email] I
get the following:
Your message to Gmod-gbrowse awaits moderator approval

Yes I have apache installed and running and the error log shows
"Permission denied: [client 127.0.0.1:46351] AH00132: file permissions
deny server access: /var/www/html/gbrowse/gmod_cog.jpeg, referer:
http://localhost/gbrowse/" when I try http://localhost/gbrowse2/yeast.

Regards
Umay Kulsum
PhD student
AIIMS

On Tue, Aug 12, 2014 at 6:13 PM, Scott Cain <[hidden email]> wrote:
> Hi Umay,
>
> Please always ask questions like this on the GBrowse mailing list (cc'ed
> here).
>
> Do you have apache installed and running?  What is in the apache error log
> (probably in /var/log/apache2/error_log)?
>
> Scott
>
>
>
> On Tue, Aug 12, 2014 at 1:45 AM, umay kulsum <[hidden email]> wrote:
>>
>> hello Scott,
>>
>> I have installed gbrowse2 via CPAN shell using the command in ubuntu
>> 14.04:
>>
>> sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
>>
>> but the example file of yeast not working with the url
>> http://localhost/gbrowse2/yeast
>> it shows the error the rquested url was not found on this server.
>>
>> all the files are installed at default locations such as:
>> /usr/lib/cgi-bin/gb2/gbrowse
>> /etc/gbrowse2/GBrowse.conf
>>
>> but nothing is found in /var/tmp/gbrowse2
>>
>> Can you please help in solving this.
>>
>> Regards
>>
>> Umay Kulsum
>> PhD Student
>> AIIMS
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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