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GBrowse2 tracks not rendering correctly

kate coyle
Hello,

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

[hidden email]
<a href="tel:%28973%29%20270-3951" value="+19732703951" target="_blank">(973) 270-3951

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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gbrowse2_screenshot.png (107K) Download Attachment
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Re: GBrowse2 tracks not rendering correctly

Scott Cain
Hi 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


On Tue, May 24, 2016 at 3:19 PM, kate coyle <[hidden email]> wrote:
Hello,

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

[hidden email]
<a href="tel:%28973%29%20270-3951" value="+19732703951" target="_blank">(973) 270-3951

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: GBrowse2 tracks not rendering correctly

kate coyle
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!

On Tue, May 24, 2016 at 4:42 PM, Scott Cain <[hidden email]> wrote:
Hi 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


On Tue, May 24, 2016 at 3:19 PM, kate coyle <[hidden email]> wrote:
Hello,

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

[hidden email]
<a href="tel:%28973%29%20270-3951" value="+19732703951" target="_blank">(973) 270-3951

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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



--
Kaitlin Coyle
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University

[hidden email]

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

GBrowse.conf (12K) Download Attachment
volvox.conf (1K) Download Attachment
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Re: GBrowse2 tracks not rendering correctly

Scott Cain
Hi Kate,

This sounds similar to what's discussed here:


Scott


On Tue, May 24, 2016 at 5:35 PM, kate coyle <[hidden email]> wrote:
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!

On Tue, May 24, 2016 at 4:42 PM, Scott Cain <[hidden email]> wrote:
Hi 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


On Tue, May 24, 2016 at 3:19 PM, kate coyle <[hidden email]> wrote:
Hello,

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

[hidden email]
<a href="tel:%28973%29%20270-3951" value="+19732703951" target="_blank">(973) 270-3951

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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



--
Kaitlin Coyle
PhD Candidate
Roberts Lab
Program in Genetics
North Carolina State University

[hidden email]



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

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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