/cgi-bin/ issue - Ubuntu

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/cgi-bin/ issue - Ubuntu

Alessandro Rossoni-2
Dear GBrowse support team,
After some days of struggle and searching the internet, I am writing to you about my problem while trying to get GBrowse2 working properly.

I have tried installing GBrowse on Ubuntu 12.04 and 14.04. In both cases I encountered the same issue. I always get the following message:

"The requested URL /cgi-bin/gbrowse2/gbrowse/volvox was not found on this server." (404 Not Found)
or
"The requested URL /cgi-bin/gb2/gbrowse/yeast was not found on this server." (404 Not Found)

However, when a collegue of mine tried to install GBrowse2 on Debian (following the same installation procedure as described in the HOWTOS) everything instantly works. Unfortunately our server works with Ubuntu.

I also attached the apache2 error log, although today (10/21) no new error was reported (and I experimented a lot)

Thanks in advance for your help.
Alessandro Rossoni


Plant Biochemisty, AG Weber
Heinrich Heine Universitaet Duesseldorf
Germany

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error.log (2K) Download Attachment
access.log (57K) Download Attachment
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Re: /cgi-bin/ issue - Ubuntu

Scott Cain
Hi Alessandro,

Please keep the mailing list cc'ed so other people can help too and the resolution gets archived.

I suspect there is something wrong with your apache config.  The GBrowse installer should have installed an apache config file called gbrowse2.conf.  In Ubuntu 12.04 systems, it would go in /etc/apache2/conf.d/.  I'm not sure if that's where it would have gone in 14.04 since the apache configuration changed somewhat between those releases.  Please verify that that the file is present and then restart apache to make sure it gets included in the configuration.

In that configuration file there should be a section telling apache how to handle the GBrowse cgis in /usr/lib/cgi-bin/gb that looks like this:

<Directory "/usr/lib/cgi-bin/gb2">

  Options ExecCGI
  SetEnv GBROWSE_CONF   "/etc/gbrowse2"
</Directory>

Scott


On Tue, Oct 21, 2014 at 3:45 PM, Alessandro Rossoni <[hidden email]> wrote:
Hi Scott, 
thank you very much for your quick answer!

I followed the steps described here:

so the command should be 
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'

I attached two screenshots.

Thanks,
Alessandro


Plant Biochemisty, AG Weber
Heinrich Heine Universitaet Duesseldorf
Germany





Date: Tue, 21 Oct 2014 15:22:02 -0400
Subject: Re: [Gmod-gbrowse] /cgi-bin/ issue - Ubuntu
From: [hidden email]
To: [hidden email]


Hi Heinrich,

Can you tell us if you were trying to install via the command line, CPAN shell or apt-get?  If you're trying to use apt-get, can you do an ls -R in your /usr/lib/cgi-bin directory?

Thanks,
Scott


On Tue, Oct 21, 2014 at 2:56 PM, Alessandro Rossoni <[hidden email]> wrote:
Dear GBrowse support team,
After some days of struggle and searching the internet, I am writing to you about my problem while trying to get GBrowse2 working properly.

I have tried installing GBrowse on Ubuntu 12.04 and 14.04. In both cases I encountered the same issue. I always get the following message:

"The requested URL /cgi-bin/gbrowse2/gbrowse/volvox was not found on this server." (404 Not Found)
or
"The requested URL /cgi-bin/gb2/gbrowse/yeast was not found on this server." (404 Not Found)

However, when a collegue of mine tried to install GBrowse2 on Debian (following the same installation procedure as described in the HOWTOS) everything instantly works. Unfortunately our server works with Ubuntu.

I also attached the apache2 error log, although today (10/21) no new error was reported (and I experimented a lot)

Thanks in advance for your help.
Alessandro Rossoni


Plant Biochemisty, AG Weber
Heinrich Heine Universitaet Duesseldorf
Germany

------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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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