You need to access gbrowse via a fcgid link. For example:<div><br></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><IfModule mod_fcgid.c></div></div>
<div><div> Alias /fgb2 "/usr/lib/cgi-bin/gb2"</div></div><div><div> <Location /fgb2></div></div><div><div> SetHandler fcgid-script</div></div><div><div> Options ExecCGI</div></div><div><div>
</Location></div></div><div><div> DefaultInitEnv GBROWSE_CONF /etc/gbrowse2</div></div><div><div></IfModule></div></div></blockquote><div><div><br></div><div>Now, provided that gbrowse is in physical directory /usr/lib/cgi-bin/gb2, you should be able to access it as URL <a href="http://your.host/fgb2/gbrowse">http://your.host/fgb2/gbrowse</a> and you will see a performance speed up.</div>
<div><br></div><div>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.</div>
<div><br></div><div>Lincoln</div><br><div class="gmail_quote">On Thu, Jul 22, 2010 at 1:36 AM, <span dir="ltr"><<a href="mailto:donghe@caltech.edu">donghe@caltech.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Dave,<br>
<br>
I re-installed everything in my developing box, now, FCGI works, however<br>
the Gbrowse2 still responses slowly, FCGI only saves scripts loading time,<br>
the searching time is still too long because thousands of scaffolds are<br>
stored in Chado. I am trying to reduce the searching time. Do you have<br>
any suggestions?<br>
<br>
Thanks<br>
<br>
Dong<br>
<div><div></div><div class="h5"><br>
<br>
> Hello all,<br>
><br>
> I don't have FCGI experience (yet, it's on my todo list), and I couldn't<br>
> find the answer at <a href="http://fastcgi.com" target="_blank">fastcgi.com</a>.. Dong's question has been out there for a<br>
> week without a response.<br>
><br>
> Does anyone have an idea? Dong, have you resolved this problem on your<br>
> own?<br>
><br>
> Thanks,<br>
><br>
> Dave C.<br>
><br>
> On Wed, Jul 14, 2010 at 10:16 AM, <<a href="mailto:donghe@caltech.edu">donghe@caltech.edu</a>> wrote:<br>
><br>
>> Hi Scott,<br>
>><br>
>> I fellow your instruction to install mod_fcgid and fcgi-perl modules in<br>
>> my<br>
>> box, and copy that configuration stanza into my main Apache<br>
>> configuration<br>
>> file, then restart httpd, the process looks fine, only got this warning<br>
>> message:<br>
>><br>
>> ---------------------------------------------------------------------<br>
>> Starting httpd: [Wed Jul 14 10:08:37 2010] [warn] module fcgid_module is<br>
>> already loaded, skipping<br>
>><br>
>> -------------------------------------------------------------------<br>
>><br>
>> but, GBrowse's performance is same as before, and I did not find any<br>
>> fcgi<br>
>> running by using 'ps -ef | grep fcgi'.<br>
>><br>
>> How to know if fastcgi is being using instead of cgi?<br>
>><br>
>> Thanks<br>
>><br>
>> Dong<br>
>><br>
>><br>
>><br>
>><br>
>><br>
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>><br>
><br>
><br>
><br>
> --<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>
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