Re: [Gmod-gbrowse] Gmod-gbrowse Digest, Vol 48, Issue 40

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Re: [Gmod-gbrowse] Gmod-gbrowse Digest, Vol 48, Issue 40

Jayaraman, Pushkala
Hello,
I used to get similar statements in my log file when I used
mod_fastcgi.. I think this is just the way Fast Cgi reports..
Otherwise I think it will say "an Error occurred"

Pushkala

Message: 1
Date: Mon, 17 May 2010 12:02:15 +0100
From: Keiran Raine <[hidden email]>
Subject: [Gmod-gbrowse] gbrowse2 - fast-cgi query
To: gbrowse List <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

Hi all,

I've just moved across to use fast-cgi instead of modperl and I'm  
slightly confused by some of the output in the error logs.

All of the stderr messages indicate:

/usr/lib/cgi-bin/gb2/gbrowse

instead of the area defined via an alias:

/gbrowse/usr/lib/cgi-bin/gb2/gbrowse

e.g.
[error] [client xx] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse"  
stderr: [3803] add_user_tracks() at /gbrowse/lib/perl/5.10.0/Bio/
Graphics/Browser2/Render.pm line 187., referer:
http://cgp-gbrowse.internal.sanger.ac.uk/fgb2/gbrowse/kr2/

I suppose my question is really is this actually a misconfiguration  
issue, of just the way that fast-cgi reports.

I've included my config below.

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
[hidden email]


FastCgiConfig  -initial-env GBROWSE_CONF=/gbrowse/etc/gbrowse2 -
initial-env PERL5LIB=/gbrowse/share/perl:/gbrowse/lib/perl/5.10.0

<VirtualHost *:80>
        ServerAdmin [hidden email]
        SetEnv PERL5LIB /gbrowse/share/perl:/gbrowse/lib/perl/5.10.0
       
        DocumentRoot /gbrowse/var/www/
        <Directory />
                Options FollowSymLinks
                AllowOverride None
        </Directory>
        <Directory /gbrowse/var/www/>
                Options Indexes FollowSymLinks MultiViews
                AllowOverride None
                Order allow,deny
                allow from all
        </Directory>

        ScriptAlias /cgi-bin/ /gbrowse/usr/lib/cgi-bin/
        <Directory "/gbrowse/usr/lib/cgi-bin">
                AllowOverride None
                Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
                Order allow,deny
                Allow from all
        </Directory>

        ErrorLog /var/log/apache2/error.log

        # Possible values include: debug, info, notice, warn, error,
crit,
        # alert, emerg.
        LogLevel warn

        CustomLog /var/log/apache2/access.log combined

     Alias /doc/ "/usr/share/doc/"
     <Directory "/usr/share/doc/">
         Options Indexes MultiViews FollowSymLinks
         AllowOverride None
         Order deny,allow
         Deny from all
         Allow from 127.0.0.0/255.0.0.0 ::1/128
     </Directory>

     Alias        "/gbrowse2/i/" "/gbrowse/var/tmp/gbrowse2/images/"
     Alias        "/gbrowse2"    "/gbrowse/var/www/gbrowse2"
     ScriptAlias  "/gb2"      "/gbrowse/usr/lib/cgi-bin/gb2"

     <Directory "/gbrowse/var/www/gbrowse2">
        Options -Indexes -MultiViews +FollowSymLinks
     </Directory>

     <Directory "/gbrowse/usr/lib/cgi-bin/gb2">
        SetEnv GBROWSE_CONF   "/gbrowse/etc/gbrowse2"
     </Directory>

     <IfModule mod_fcgid.c>
         Alias /fgb2/ "/gbrowse/usr/lib/cgi-bin/gb2/"
         PerlRequire /gbrowse/lib/apache_startup.pl
         <Location /fgb2>
           SetHandler   fcgid-script
           Options      ExecCGI
         </Location>
     </IfModule>
</VirtualHost>


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
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