[Gmod-gbrowse] 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

[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

Post by 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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[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

Dear Scott
Thank you for your reply. I have made thing worst now. I could not open
'The server encountered an internal error or misconfiguration and was
unable to complete your request.
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.'
-----------------------------------------------------------
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
http://localhost/cgi-bin/gbrowse/gbrowse/volvox/
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
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
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
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

Post by 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

Post by 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
------------------------------------------------------------------------------
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
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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