[Gmod-gbrowse] gbrowse2 - fast-cgi query

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[Gmod-gbrowse] gbrowse2 - fast-cgi query

Keiran Raine
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


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 compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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