features are not displayed

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features are not displayed

Qisen Zhang
Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen


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Re: features are not displayed

Scott Cain
Hi Qisen,

Can you please send a screenshot of what your browser looks like as well as anything in your apache error log that looks like it might be related to GBrowse?

Scott



On Sun, Apr 13, 2014 at 3:14 AM, Qisen Zhang <[hidden email]> wrote:
Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen


------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research

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this first edition is now available. Download your free book today!
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Re: features are not displayed

Scott Cain
Hi Qisen,

Always reply-all so the GBrowse mailing list stays cc'ed.

How did you install GBrowse?  The beginning of your error log mentions a url that has "...gbrowse/gbrowse/volvox" in it, which is the url I would expect from a apt-get install, but the end of your conf file mentions the file path /var/lib/gbrowse2, which is a path I would expect if it were installed on the command line (either from a downloaded tarball, a git clone or the cpan shell).

My guess is that you initially installed via apt-get, had some problem, then installed via the cpan shell, and now you have both.  I agree that there is a permission problem on the session directory; you should make sure it's owned by the apache user:

  sudo chown www-data:www-data /var/lib/gbrowse2/sessions


Scott





On Mon, Apr 14, 2014 at 11:20 PM, Qisen Zhang <[hidden email]> wrote:
Dear Scott
Thank you for your reply. I have made thing worst now. I could not open the page any more. Just get following error:

'The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.'

and error log file has following contents:

-----------------------------------------------------------
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
[Tue Apr 15 12:07:17 2014] [error] [client 127.0.0.1] File does not exist: /var/www/gbrowse, referer: http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:07:25 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:10:32 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:15:56 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse
couldn't create lock file '/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at /usr/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 15 12:39:33 2014] [error] [client 127.0.0.1] Premature end of script headers: gbrowse"

I am not good on using Ubuntu system. I may have file access permission problems.

Would you help please?

Best Regards

Qisen



On Mon, Apr 14, 2014 at 11:25 PM, Scott Cain <[hidden email]> wrote:
Hi Qisen,

Can you please send a screenshot of what your browser looks like as well as anything in your apache error log that looks like it might be related to GBrowse?

Scott



On Sun, Apr 13, 2014 at 3:14 AM, Qisen Zhang <[hidden email]> wrote:
Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen


------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse