Hi Scott,
Thanks for the prompt reply!
Here's my apache error log. I restarted apache earlier today for something
unrelated to this. The last few errors are from while I was doing the
tutorial--I think there's a typo that directs users to
http://localhost/cgi-bin/gbrowse2/gbrowse/volvox when it should be
directing to http://localhost/cgi-bin/gb2/gbrowse/volvox. I don't see
anything here that would indicate where it's getting hung up...
[Mon May 23 07:51:25.504076 2016] [mpm_prefork:notice] [pid 32466] AH00163:
Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.16 mod_perl/2.0.8
Perl/v5.18.2 configured -- resuming normal operations
[Mon May 23 07:51:25.504096 2016] [core:notice] [pid 32466] AH00094:
Command line: '/usr/sbin/apache2'
[Tue May 24 14:30:23.379923 2016] [mpm_prefork:notice] [pid 32466] AH00173:
SIGHUP received. Attempting to restart
[Tue May 24 14:30:23.658590 2016] [mpm_prefork:notice] [pid 32466] AH00163:
Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.16 mod_perl/2.0.8
Perl/v5.18.2 configured -- resuming normal operations
[Tue May 24 14:30:23.658607 2016] [core:notice] [pid 32466] AH00094:
Command line: '/usr/sbin/apache2'
[Tue May 24 14:39:38.937569 2016] [cgi:error] [pid 3284] [client
127.0.0.1:54828] script not found or unable to stat:
/usr/lib/cgi-bin/gbrowse2
[Tue May 24 14:39:54.511123 2016] [cgi:error] [pid 3291] [client
127.0.0.1:54829] script not found or unable to stat:
/usr/lib/cgi-bin/gbrowse2
[Tue May 24 14:52:57.657444 2016] [cgi:error] [pid 3291] [client
127.0.0.1:54852] script not found or unable to stat:
/usr/lib/cgi-bin/gbrowse2
Configuration files are attached.
I was poking around in chrome and "Inspecting" the running site, and it
looks like it's pulling images from gbrowse2/i/volvox, which is in
/var/www/html. I can see the png files in that folder.
I also noticed that the features in the Example Features track are still
there and clickable (the info bubble even pops up when I hover over them).
It's just not rendering the image itself.
Thanks!
Post by Scott CainHi Kate,
I would say that GBrowse/apache can't find where the images are, or they
aren't being created. Please take a look at the apache error log (probably
/var/log/apache2/error_log) and go to the bottom of it and look for 404
errors that would indicate that it can't find the images, and then you/we
will need to sort out why they aren't getting created there. When you
reply, you can included the last several lines of your apache error log and
the configuration files you're using (GBrowse.conf and volvox.conf) so we
can take a look at those too.
Scott
Post by kate coyleHello,
I'm trying to set up GBrowse2 on my computer. I was working through the
Tutorial for Administrators, but have run into an issue I can't seem to
solve. The tracks aren't rendering properly--see attached.
I've gone through all the suggested steps to ensure that all the
necessary files are universally accessible. There are no new entries in my
apache error log file. I've also accessed the web server from another
computer (a Windows machine) to check if it was an issue with graphics on
my ubuntu server, but the tracks look the same.
Do you have any suggestions as to how to proceed or what might be going
wrong?
Thanks!
Kate Coyle
--
*Kaitlin Coyle*
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University
(973) 270-3951
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Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
*Kaitlin Coyle*
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University
***@ncsu.edu