Issue with tutorial and features

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Issue with tutorial and features

gtoth
As described in a Feb 26 post, features are not appearing for the volvox
tutorial.  I get the error "MSG: No suitable files found in
/var/lib/gbrowse2/databases/volvox," amongst others (I've checked the
ownership and permissions).  However, when at
http://localhost/cgi-bin/gb2/gbrowse/volvox I can use the little red box
with the balloon "Configure this track", and get a dialog box with a
"Change" button which then reveals the features (everything in the dialog
box works).  Editing the volvox.conf file changes the defaults in this
dialogue box.  Seems that there's some general configuration issue?



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Re: Issue with tutorial and features

Scott Cain
Hi,

I don't think that is a general configuration issue.  Perhaps there is something going on with image caching?  GBrowse on the server side (not in the browser) is pretty aggressive about caching images that it already created so that it won't have to create them again.  This is great for users as it can make things faster, but a pain for administrators who are trying to test things and changing the contents of files (so perhaps the appropriate file wasn't there at one point, gbrowse created an empty image, you put the appropriate file in place and looked at the same place in the browse, where GBrowse realized that it shouldn't have to redraw the picture because it already drew that picture (that is, it doesn't know you added data)).

So, when you're doing the tutorial, make sure to use the "update appearance" button in the preferences tab whenever you change the data or configuration file.  Also, zooming or panning to a different location can help too.

Scott



On Thu, Mar 20, 2014 at 6:19 PM, gtoth <[hidden email]> wrote:
As described in a Feb 26 post, features are not appearing for the volvox
tutorial.  I get the error "MSG: No suitable files found in
/var/lib/gbrowse2/databases/volvox," amongst others (I've checked the
ownership and permissions).  However, when at
http://localhost/cgi-bin/gb2/gbrowse/volvox I can use the little red box
with the balloon "Configure this track", and get a dialog box with a
"Change" button which then reveals the features (everything in the dialog
box works).  Editing the volvox.conf file changes the defaults in this
dialogue box.  Seems that there's some general configuration issue?



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------------------------------------------------------------------------------
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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/13534_NeoTech
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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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/13534_NeoTech
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Re: Issue with tutorial and features

gtoth

Scott,

 

Thanks for the response.  You mention using the “preferences” tab.  I assume you’re referring to the tabs that I’ve drawn a box around on the attached screen shot.  These tabs are not active.

 

Greg

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, March 21, 2014 12:25 PM
To: Toth, Greg
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Issue with tutorial and features

 

Hi,

 

I don't think that is a general configuration issue.  Perhaps there is something going on with image caching?  GBrowse on the server side (not in the browser) is pretty aggressive about caching images that it already created so that it won't have to create them again.  This is great for users as it can make things faster, but a pain for administrators who are trying to test things and changing the contents of files (so perhaps the appropriate file wasn't there at one point, gbrowse created an empty image, you put the appropriate file in place and looked at the same place in the browse, where GBrowse realized that it shouldn't have to redraw the picture because it already drew that picture (that is, it doesn't know you added data)).

 

So, when you're doing the tutorial, make sure to use the "update appearance" button in the preferences tab whenever you change the data or configuration file.  Also, zooming or panning to a different location can help too.

 

Scott

 

 

On Thu, Mar 20, 2014 at 6:19 PM, gtoth <[hidden email]> wrote:

As described in a Feb 26 post, features are not appearing for the volvox
tutorial.  I get the error "MSG: No suitable files found in
/var/lib/gbrowse2/databases/volvox," amongst others (I've checked the
ownership and permissions).  However, when at
http://localhost/cgi-bin/gb2/gbrowse/volvox I can use the little red box
with the balloon "Configure this track", and get a dialog box with a
"Change" button which then reveals the features (everything in the dialog
box works).  Editing the volvox.conf file changes the defaults in this
dialogue box.  Seems that there's some general configuration issue?



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View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Issue-with-tutorial-and-features-tp5712381.html
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------------------------------------------------------------------------------
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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/13534_NeoTech
_______________________________________________
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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


------------------------------------------------------------------------------
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/13534_NeoTech
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Re: Issue with tutorial and features

Scott Cain
Hi Greg,

Are you blocking javascript?  The text there should be links, and I also see that there are JS controls missing from the tracks.  Can you check the apache error log for messages about missing files?  The most likely problem is that something happened during the installation and the files didn't go where they were supposed to go.

Scott



On Fri, Mar 21, 2014 at 9:00 PM, Toth, Greg <[hidden email]> wrote:

Scott,

 

Thanks for the response.  You mention using the “preferences” tab.  I assume you’re referring to the tabs that I’ve drawn a box around on the attached screen shot.  These tabs are not active.

 

Greg

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, March 21, 2014 12:25 PM
To: Toth, Greg
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Issue with tutorial and features

 

Hi,

 

I don't think that is a general configuration issue.  Perhaps there is something going on with image caching?  GBrowse on the server side (not in the browser) is pretty aggressive about caching images that it already created so that it won't have to create them again.  This is great for users as it can make things faster, but a pain for administrators who are trying to test things and changing the contents of files (so perhaps the appropriate file wasn't there at one point, gbrowse created an empty image, you put the appropriate file in place and looked at the same place in the browse, where GBrowse realized that it shouldn't have to redraw the picture because it already drew that picture (that is, it doesn't know you added data)).

 

So, when you're doing the tutorial, make sure to use the "update appearance" button in the preferences tab whenever you change the data or configuration file.  Also, zooming or panning to a different location can help too.

 

Scott

 

 

On Thu, Mar 20, 2014 at 6:19 PM, gtoth <[hidden email]> wrote:

As described in a Feb 26 post, features are not appearing for the volvox
tutorial.  I get the error "MSG: No suitable files found in
/var/lib/gbrowse2/databases/volvox," amongst others (I've checked the
ownership and permissions).  However, when at
http://localhost/cgi-bin/gb2/gbrowse/volvox I can use the little red box
with the balloon "Configure this track", and get a dialog box with a
"Change" button which then reveals the features (everything in the dialog
box works).  Editing the volvox.conf file changes the defaults in this
dialogue box.  Seems that there's some general configuration issue?



--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Issue-with-tutorial-and-features-tp5712381.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
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/13534_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/13534_NeoTech
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Re: Issue with tutorial and features

gtoth

Scott,

 

Again, thanks for your response.

 

Yes, Javascript is enabled on IE9.  However, I switched to Chrome and the tabs, features and other page options appeared.  I was able to go through the tutorial changing volvox.conf to edit the remarks, motifs and names with some minor hang-ups (search found three elements for HGA, but not Protein:HGA)(there is no volvox2b.gff3 in any directory).  However, in the error_log I still get “MSG: No suitable files found in /var/lib/gbrowse2/databases/volvox, referer: http://h2626uohpk504.cin.epa.gov/cgi-bin/gb2/gbrowse/volvox/?name=ctgA” (now I’m getting it three times, I assume once for each file it’s trying to find in the volvox directory).

 

Given that my main interest has been in learning to use Chado for annotation management and my next move was to install Chado and Apollo (i.e., doing the GMOD 2nd case study), I’m concerned that there’s still something that happened during the Gbrowse installation (as you mentioned).  I’ve attached two files – one (Gbrowse2_install_gt) that shows the “Exceptions” that I got during the ./Build test (even though the result was “All tests successful”, and a second (Error_log_gt) that shows the current “error_log” that results from http://localhost/cgi-bin/gb2/gbrowse/volvox/?name=ctgA being run.

 

Thanks,

Greg

 

By the way Drupal and Tripal 2.0 are running fine (installed and tutorial successful).  Some talk of Gbrowse being integrated into Tripal 2.0?

 

Additional information

The installation directories are as follows:

Directory for GBrowse's config and support files? [/etc/gbrowse2]

Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2]

Directory for GBrowse's temporary data [/var/tmp/gbrowse2]

Directory for GBrowse's sessions, uploaded tracks and other persistent data [/var/lib/gbrowse2]

Directory for GBrowse's example databases [/var/lib/gbrowse2/databases]

Directory for GBrowse's CGI script executables? [/var/www/html/gbrowse2/cgi-bin/gb2]

Internet port to run demo web site on (for demo)? [8000]

Apache loadable module directory (for demo)? [/etc/httpd/modules]

User account under which Apache daemon runs? [apache]

Automatically update Apache config files to run GBrowse? [y]

Automatically update system config files to run gbrowse-slave? [y]

 

Directories and files relevant to the tutorial have ownership gtoth:apache ; permissions set at 776

PHP version: 5.3.3

RHEL 6

Perl version: 5.10.1

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, March 21, 2014 9:25 PM
To: Toth, Greg
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Issue with tutorial and features

 

Hi Greg,

 

Are you blocking javascript?  The text there should be links, and I also see that there are JS controls missing from the tracks.  Can you check the apache error log for messages about missing files?  The most likely problem is that something happened during the installation and the files didn't go where they were supposed to go.

 

Scott

 

 

On Fri, Mar 21, 2014 at 9:00 PM, Toth, Greg <[hidden email]> wrote:

Scott,

 

Thanks for the response.  You mention using the “preferences” tab.  I assume you’re referring to the tabs that I’ve drawn a box around on the attached screen shot.  These tabs are not active.

 

Greg

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, March 21, 2014 12:25 PM
To: Toth, Greg
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Issue with tutorial and features

 

Hi,

 

I don't think that is a general configuration issue.  Perhaps there is something going on with image caching?  GBrowse on the server side (not in the browser) is pretty aggressive about caching images that it already created so that it won't have to create them again.  This is great for users as it can make things faster, but a pain for administrators who are trying to test things and changing the contents of files (so perhaps the appropriate file wasn't there at one point, gbrowse created an empty image, you put the appropriate file in place and looked at the same place in the browse, where GBrowse realized that it shouldn't have to redraw the picture because it already drew that picture (that is, it doesn't know you added data)).

 

So, when you're doing the tutorial, make sure to use the "update appearance" button in the preferences tab whenever you change the data or configuration file.  Also, zooming or panning to a different location can help too.

 

Scott

 

 

On Thu, Mar 20, 2014 at 6:19 PM, gtoth <[hidden email]> wrote:

As described in a Feb 26 post, features are not appearing for the volvox
tutorial.  I get the error "MSG: No suitable files found in
/var/lib/gbrowse2/databases/volvox," amongst others (I've checked the
ownership and permissions).  However, when at
http://localhost/cgi-bin/gb2/gbrowse/volvox I can use the little red box
with the balloon "Configure this track", and get a dialog box with a
"Change" button which then reveals the features (everything in the dialog
box works).  Editing the volvox.conf file changes the defaults in this
dialogue box.  Seems that there's some general configuration issue?



--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Issue-with-tutorial-and-features-tp5712381.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
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/13534_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" 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/13534_NeoTech
_______________________________________________
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GBrowse2 install_gt.docx (31K) Download Attachment
Error_log_gt.docx (19K) Download Attachment