[Gmod-tripal-devel] GBrowse fcgi and Drupal

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[Gmod-tripal-devel] GBrowse fcgi and Drupal

Scott Cain
Hi All,

I'm trying to use the GBrowse fastcgi config on a machine that has Drupal/Tripal installed.  The apache config for GBrowse/fastcgi has an alias for the GBrowse cgi directory set to /fgb2, so that one would access GBrowse with a url like http://localhost/fgb2/gbrowse/yeast. The problem is that drupal intercepts this url and gives my "file not found".  Is there something I can put in the .htaccess file to keep this from happening?  I feel like I should figure this out on my own, but .htaccess files always feel like black magic to me, so I'd rather talk to a magician :-)

Thanks,
Scott


--
------------------------------------------------------------------------
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: [Gmod-tripal-devel] GBrowse fcgi and Drupal

Michael Dondrup-3
Hi Scott,

we have a similar setup without problems (with file not found interception from Drupal at least ;)
We didn't have to do anything with the .htaccess files. We have a virtual host, configured to
https://lb-test.bccs.uib.no and the Document root is set to the Drupal installation directory.
Then we have a config file for gbrowse using the same server name and some configuration
stanzas copied from the file that the gbrowse installation generates.
...
<IfModule mod_fcgid.c>
  Alias /fgb2 "/licebase/httpd/cgi-bin/gbrowse2"
  <Location /fgb2>
    SetHandler   fcgid-script
  </Location>
  DefaultInitEnv GBROWSE_CONF /licebase//etc/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  DefaultMinClassProcessCount 6
  IPCCommTimeout   600
  BusyTimeout 600
</IfModule>
….

My bet is, that the module mod_fcgid is not really loaded or the handler is not activated, or that the gbrowse config is
not loaded at all.

Hope this helps
Michael
 



On May 17, 2013, at 5:36 PM, Scott Cain wrote:

> Hi All,
>
> I'm trying to use the GBrowse fastcgi config on a machine that has Drupal/Tripal installed.  The apache config for GBrowse/fastcgi has an alias for the GBrowse cgi directory set to /fgb2, so that one would access GBrowse with a url like http://localhost/fgb2/gbrowse/yeast. The problem is that drupal intercepts this url and gives my "file not found".  Is there something I can put in the .htaccess file to keep this from happening?  I feel like I should figure this out on my own, but .htaccess files always feel like black magic to me, so I'd rather talk to a magician :-)
>
> Thanks,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d_______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
AlienVault Unified Security Management (USM) platform delivers complete
security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
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Re: [Gmod-tripal-devel] GBrowse fcgi and Drupal

Scott Cain
Hi Michael,

I can't believe it: "is it plugged in?" wins the day.  I forgot to install fcgid; I installed libfcgi-perl and thought I was done.  I had to install libapache2-mod-fcgid and restart apache.  Thanks!

Scott



On Fri, May 17, 2013 at 1:04 PM, Michael Dondrup <[hidden email]> wrote:
Hi Scott,

we have a similar setup without problems (with file not found interception from Drupal at least ;)
We didn't have to do anything with the .htaccess files. We have a virtual host, configured to
https://lb-test.bccs.uib.no and the Document root is set to the Drupal installation directory.
Then we have a config file for gbrowse using the same server name and some configuration
stanzas copied from the file that the gbrowse installation generates.
...
<IfModule mod_fcgid.c>
  Alias /fgb2 "/licebase/httpd/cgi-bin/gbrowse2"
  <Location /fgb2>
    SetHandler   fcgid-script
  </Location>
  DefaultInitEnv GBROWSE_CONF /licebase//etc/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  DefaultMinClassProcessCount 6
  IPCCommTimeout   600
  BusyTimeout 600
</IfModule>
….

My bet is, that the module mod_fcgid is not really loaded or the handler is not activated, or that the gbrowse config is
not loaded at all.

Hope this helps
Michael




On May 17, 2013, at 5:36 PM, Scott Cain wrote:

> Hi All,
>
> I'm trying to use the GBrowse fastcgi config on a machine that has Drupal/Tripal installed.  The apache config for GBrowse/fastcgi has an alias for the GBrowse cgi directory set to /fgb2, so that one would access GBrowse with a url like http://localhost/fgb2/gbrowse/yeast. The problem is that drupal intercepts this url and gives my "file not found".  Is there something I can put in the .htaccess file to keep this from happening?  I feel like I should figure this out on my own, but .htaccess files always feel like black magic to me, so I'd rather talk to a magician :-)
>
> Thanks,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d_______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




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

------------------------------------------------------------------------------
AlienVault Unified Security Management (USM) platform delivers complete
security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel