[Gmod-help] Re: [Gmod-gbrowse] Running GBrowse under FastCGI

[Lincoln Stein]

You need to access gbrowse via a fcgid link. For example:

<IfModule mod_fcgid.c>
  Alias /fgb2 "/usr/lib/cgi-bin/gb2"
  <Location /fgb2>
    SetHandler   fcgid-script
    Options      ExecCGI
  </Location>
  DefaultInitEnv GBROWSE_CONF /etc/gbrowse2
</IfModule>


Now, provided that gbrowse is in physical directory /usr/lib/cgi-bin/gb2,
you should be able to access it as URL http://your.host/fgb2/gbrowse and you
will see a performance speed up.

if you have thousands of scaffolds in a flat file and are trying to load
them using the memory adaptor, you shouldn't do that! Please load them into
a mysql, postgres or sqlite database. This will increase the speed
immensely. You can also use a BigBed file for this purpose.

Lincoln

On Thu, Jul 22, 2010 at 1:36 AM, <donghe at caltech.edu> wrote:

> Hi Dave,
>
> I re-installed everything in my developing box, now, FCGI works, however
> the Gbrowse2 still responses slowly, FCGI only saves scripts loading time,
> the searching time is still too long because thousands of scaffolds are
> stored in  Chado. I am trying to reduce the searching time. Do you have
> any suggestions?
>
> Thanks
>
> Dong
>
>
> > Hello all,
> >
> > I don't have FCGI experience (yet, it's on my todo list), and I couldn't
> > find the answer at fastcgi.com..  Dong's question has been out there for
> a
> > week without a response.
> >
> > Does anyone have an idea?  Dong, have you resolved this problem on your
> > own?
> >
> > Thanks,
> >
> > Dave C.
> >
> > On Wed, Jul 14, 2010 at 10:16 AM, <donghe at caltech.edu> wrote:
> >
> >> Hi Scott,
> >>
> >> I fellow your instruction to install mod_fcgid and fcgi-perl modules in
> >> my
> >> box, and copy that configuration stanza into my main Apache
> >> configuration
> >> file, then restart httpd, the process looks fine, only got this warning
> >> message:
> >>
> >> ---------------------------------------------------------------------
> >> Starting httpd: [Wed Jul 14 10:08:37 2010] [warn] module fcgid_module is
> >> already loaded, skipping
> >>
> >> -------------------------------------------------------------------
> >>
> >> but, GBrowse's performance is same as before, and I did not find any
> >> fcgi
> >> running by using 'ps -ef | grep fcgi'.
> >>
> >> How to know if fastcgi is being using instead of cgi?
> >>
> >> Thanks
> >>
> >> Dong
> >>
> >>
> >>
> >>
> >>
> >>
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> >>
> >
> >
> >
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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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