Thank you for the suggestions.

I am installing Gbrowse2.39 on an old Dell desktop running RedHat Enterprise Linux 5.1.19.6 which also lists Red Hat linux 2.6.18-274.el5 as it boots.

When I build the demo as you suggested, I can connect and it does work. I turned it off and then I rebuilt my bioperl and dependencies and tried to delete all the GB2 directories then rebult GB2. At the end of this GB2 rebuild I see:

All tests successful.
Files=9, Tests=439, 69 wallclock secs ( 0.29 usr  0.05 sys + 37.99 cusr  7.17 csys = 45.50 CPU)
Result: PASS

Connecting to this fresh GB2  ( <at>  http://localhost/cgi-bin/gb2) gives these lines in the error_log:

[Fri Sep 02 10:07:44 2011] [error] [client 127.0.0.1] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/lib/perl5/site_perl/5.8.8/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Fri Sep 02 10:07:44 2011] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html

If make  /var/lib/gbrowse2/sessions  writtable then these 'permission denied' errors are avoided but then I  return to these 'method param  undefined' errors

[Fri Sep 02 10:26:59 2011] [error] [client 128.23.6.30] Can't call method "param" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/Bio/Graphics/Browser2/Session.pm line 316., referer: http://localhost/index.html.en
[Fri Sep 02 10:26:59 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse, referer: http://localhost/index.html.en

If I then ./Build demo I can connect to  http://localhost:8000/cgi-bin/gb2/gbrowse/yeast/ and manipulate the display.

http://localhost/cgi-bin/gb2 does not work

http://localhost:8000/cgi-bin/gb2/ does work


So I'm stumped at the moment.


Starr

From: Lincoln Stein [lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org]
Sent: Wednesday, August 31, 2011 11:50 AM
To: Hazard, E. Starr
Cc: gmod-gbrowse <at> lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] trouble with session and param method

Could you try the following from within the distribution directory:

 perl Build.PL
 ./Build clean
 ./Build demo

Then try to connect to the demo server (the URL will print out when you run Build demo).

I do not know what's going on, but this procedure will ensure that you don't have any conflicting libraries or configuration directives from within GBrowse. Also you didn't mention what operating system/distribution you're using.

Lincoln

On Tue, Aug 30, 2011 at 5:39 PM, Hazard, E. Starr <hazards-sm4NYSCnXRo@public.gmane.org<mailto:hazards-sm4NYSCnXRo@public.gmane.org>> wrote:
Folks,

I have been trying to get an instance GBrowse2 up and running. I had a screen showing at one point but clicking on any objects to change gave a series of errors[

Tue Aug 30 15:54:06 2011] [error] [client 128.23.6.30] couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/lib/perl5/site_perl/5.8.8/CGI/Session/Driver/db_file.pm<http://db_file.pm> line 98., referer: http://pchazards-linux.csb.mu/var/lib/gbrowse2/sessions/sc.edu/cgi-bin/gb2/gbrowse/yeast/

[Tue Aug 30 15:54:06 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse, referer: http://pchazards-linux.csb.musc.edu/cgi-bin/gb2/gbrowse/yeast/

When I altered the write permission for the
/var/lib/gbrowse2/sessions/

directory began to see the following error in my apache error_log

[Tue Aug 30 17:21:45 2011] [error] [client 128.23.6.30]
Can't call method "param" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/Bio/Graphics/Browser2/Session.pm line 316., referer: http://pchazards-linux.csb.musc.edu/index.html.en
[Tue Aug 30 17:21:45 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse, referer: http://pchazards-linux.csb.musc.edu/index.html.en

I have CGI-Session-4.48 installed

here's my "z_gbrowse.conf" file content
cat /etc/httpd/conf.d/z_gbrowse2.conf
Alias        "/gbrowse2/i/" "/tmp/gbrowse2/images/"
Alias        "/gbrowse2"    "/var/www/html/gbrowse2"
ScriptAlias  "/gb2"      "/var/www/cgi-bin/gb2"

<Directory "/var/www/html/gbrowse2">
 AllowOverride Options
 Options -Indexes -MultiViews +FollowSymLinks
 Order allow,deny
 Allow from all
</Directory>

<Directory "/var/www/html/gbrowse2/tutorial">
 Options +Indexes
</Directory>

<Directory "/tmp/gbrowse2/images/">
 Order allow,deny
 Allow from all
</Directory>

<Directory "/var/lib/gbrowse2/databases">
 Order allow,deny
 Deny from all
</Directory>

<Directory "/var/www/cgi-bin/gb2">

 Options ExecCGI
 SetEnv GBROWSE_CONF   "/etc/gbrowse2"
</Directory>

<IfModule mod_fcgid.c>
 Alias /fgb2 "/var/www/cgi-bin/gb2"
 <Location /fgb2>
  SetHandler   fcgid-script
 </Location>
 FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
 # these directives prevent idle/busy timeouts and may need to be
 # adjusted up or down
 FcgidMinProcessesPerClass 6
 FcgidIOTimeout   600
 FcgidBusyTimeout 600

</IfModule>

<IfModule mod_fastcgi.c>
 Alias /fgb2 "/var/www/cgi-bin/gb2"
 <Location /fgb2>
  SetHandler   fastcgi-script
 </Location>
 # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
 # errors.
 FastCgiConfig -idle-timeout 600 -maxClassProcesses 20  -initial-env GBROWSE_CONF=/etc/gbrowse2
</IfModule>

<IfModule mod_perl.c>
 Alias /mgb2 "/var/www/cgi-bin/gb2"

 <Location /mgb2>
   SetHandler perl-script
   PerlResponseHandler ModPerl::Registry
   PerlOptions +ParseHeaders
 </Location>
</IfModule>

What should I fix to make the basic setup work?

Starr

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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-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org<mailto:Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>>