GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

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GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

by Krishna, Ritesh :: Rate this Message:

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Hi List,

 

I am trying to install Gbrowse on Fedora 11 and getting following error (pasted from Apache error log) while trying to access the yeast database as suggested in the tutorial.

 

 

[Tue Oct 27 11:17:32 2009] [error] [client xxx.xxx.xx.xx] /etc/httpd/conf/gbrowse.conf: not a directory at /usr/local/lib/perl5/site_perl/5.10.0/i386-

linux-thread-multi/Bio/Graphics/Browser/Util.pm line 152

 

 

I can see the welcome page of GBrowse on  http://xxx.xxx.xx.xx/gbrowse , but the server gives 500 internal server error as soon as in click on the 

http://xxx.xxx.xx.xx/cgi-bin/gbrowse/yeast link provided to access the yeast database.

 

I have checked that the directory ‘/etc/httpd/conf/gbrowse.conf’ does exist with the yeast configuration files.  The yeast database is also present in the default location /var/www/html/gbrowse/databases/yeast_chr1+2.

 

 

Any idea what might be going wrong with my setup?

 

Thanks a lot,

Ritesh.


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Re: GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

by Scott Cain-4 :: Rate this Message:

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Hi Ritesh,

On Fedora systems, this tends to happen when SELinux is turned on  
(which is the default with Fedora/RedHat).  Try disabling it to see if  
GBrowse works with it turned off.

Scott


On Oct 27, 2009, at 11:41 AM, Krishna, Ritesh wrote:

> Hi List,
>
> I am trying to install Gbrowse on Fedora 11 and getting following  
> error (pasted from Apache error log) while trying to access the  
> yeast database as suggested in the tutorial.
>
>
> [Tue Oct 27 11:17:32 2009] [error] [client xxx.xxx.xx.xx] /etc/httpd/
> conf/gbrowse.conf: not a directory at /usr/local/lib/perl5/site_perl/
> 5.10.0/i386-
> linux-thread-multi/Bio/Graphics/Browser/Util.pm line 152
>
>
> I can see the welcome page of GBrowse on  http://xxx.xxx.xx.xx/ 
> gbrowse , but the server gives 500 internal server error as soon as  
> in click on the
> http://xxx.xxx.xx.xx/cgi-bin/gbrowse/yeast link provided to access  
> the yeast database.
>
> I have checked that the directory ‘/etc/httpd/conf/gbrowse.conf’  
> does exist with the yeast configuration files.  The yeast database  
> is also present in the default location /var/www/html/gbrowse/
> databases/yeast_chr1+2.
>
>
> Any idea what might be going wrong with my setup?
>
> Thanks a lot,
> Ritesh.
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-----------------------------------------------------------------------
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: GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

by Krishna, Ritesh :: Rate this Message:

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Hi Scott,

Disabling the SELINUX kernel module works fine. The net installer script worked smoothly and the setup seems to be running fine with the yeast and volvox examples.

Many thanks,
Ritesh.

-----Original Message-----
From: Scott Cain [mailto:scott@...]
Sent: 27 October 2009 21:31
To: Krishna, Ritesh
Cc: 'gmod-gbrowse@...'
Subject: Re: [Gmod-gbrowse] GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

Hi Ritesh,

On Fedora systems, this tends to happen when SELinux is turned on  
(which is the default with Fedora/RedHat).  Try disabling it to see if  
GBrowse works with it turned off.

Scott


On Oct 27, 2009, at 11:41 AM, Krishna, Ritesh wrote:

> Hi List,
>
> I am trying to install Gbrowse on Fedora 11 and getting following  
> error (pasted from Apache error log) while trying to access the  
> yeast database as suggested in the tutorial.
>
>
> [Tue Oct 27 11:17:32 2009] [error] [client xxx.xxx.xx.xx] /etc/httpd/
> conf/gbrowse.conf: not a directory at /usr/local/lib/perl5/site_perl/
> 5.10.0/i386-
> linux-thread-multi/Bio/Graphics/Browser/Util.pm line 152
>
>
> I can see the welcome page of GBrowse on  http://xxx.xxx.xx.xx/ 
> gbrowse , but the server gives 500 internal server error as soon as  
> in click on the
> http://xxx.xxx.xx.xx/cgi-bin/gbrowse/yeast link provided to access  
> the yeast database.
>
> I have checked that the directory ‘/etc/httpd/conf/gbrowse.conf’  
> does exist with the yeast configuration files.  The yeast database  
> is also present in the default location /var/www/html/gbrowse/
> databases/yeast_chr1+2.
>
>
> Any idea what might be going wrong with my setup?
>
> Thanks a lot,
> Ritesh.
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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





------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
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Re: GBrowse on Fedora 11 (Apache signalling Error in Util.pm line 152)

by Matthew Hobbs-2 :: Rate this Message:

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Having found out this way that SElinux is the problem you could if you
wish re-enable it and try to fix the specific problem, which will have
been logged. I have found that setroubleshoot and its GUI client
application sealert are useful in finding the problem and the suggested
solution which may be e.g. simply restoring the default security context
for one of the gbrowse config files (this was the case with one of my
servers).

Hope this helps,

Matthew

> -----Original Message-----
> From: Krishna, Ritesh [mailto:Ritesh.Krishna@...]
> Sent: Wednesday, 28 October 2009 10:59 PM
> To: 'scott@...'
> Cc: 'gmod-gbrowse@...'
> Subject: Re: [Gmod-gbrowse] GBrowse on Fedora 11 (Apache signalling
> Error in Util.pm line 152)
>
> Hi Scott,
>
> Disabling the SELINUX kernel module works fine. The net installer
> script worked smoothly and the setup seems to be running fine with the
> yeast and volvox examples.
>
> Many thanks,
> Ritesh.
>
> -----Original Message-----
> From: Scott Cain [mailto:scott@...]
> Sent: 27 October 2009 21:31
> To: Krishna, Ritesh
> Cc: 'gmod-gbrowse@...'
> Subject: Re: [Gmod-gbrowse] GBrowse on Fedora 11 (Apache signalling
> Error in Util.pm line 152)
>
> Hi Ritesh,
>
> On Fedora systems, this tends to happen when SELinux is turned on
> (which is the default with Fedora/RedHat).  Try disabling it to see if
> GBrowse works with it turned off.
>
> Scott
>

___________________________________________
Matthew Hobbs Ph.D.
Faculty of Veterinary Science
C01 - J.L. Shute
University of Sydney, NSW 2570, Australia
Phone: +61 2 9351 1673 Fax: +61 2 9351 1693


------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
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