[Gmod-gbrowse] /cgi-bin/ issue - Ubuntu

[Alessandro Rossoni]

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

[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

Hi Scott,
thank you very much for your quick answer!
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO
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
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
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
"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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Scott Cain, Ph. D. scott at scottcain
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GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research