[Gmod-gbrowse] Assist in GMOD

[Seyed Ahmad Mousavi]

Hi

I've installed gbrowse 2.54 on Fedora 23, but during working with human
sample chr 22 and chr2 the GBrowse does not show rulers and grids. You
could see my page I got from screen.

How can I fix the problem?


Kind regards,
--
Ahmad Mousavi
Royan Institute,
Tehran, Iran

[Scott Cain]

Hi Sayed,

This problem sounds very similar to another just posted to the mailing list
(for which there is not a resolution yet but there are suggestions):

http://gmod.827538.n3.nabble.com/GBrowse2-tracks-not-rendering-correctly-td4054457.html

Also, people have had issues with newer versions of apache (2.4) discussed
here:

http://gmod.827538.n3.nabble.com/gbrowse-problem-td4053878.html

Scott


On Wed, May 25, 2016 at 10:09 AM, Seyed Ahmad Mousavi <

Post by Seyed Ahmad Mousavi
Hi
I've installed gbrowse 2.54 on Fedora 23, but during working with human
sample chr 22 and chr2 the GBrowse does not show rulers and grids. You
could see my page I got from screen.
How can I fix the problem?
Kind regards,
--
Ahmad Mousavi
Royan Institute,
Tehran, Iran
------------------------------------------------------------------------------
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
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Scott Cain]

Hi Ahmad,

I'm guessing that since you sent me another email with a question after
this one that the database connectivity problems have been solved, yes?

Scott


On Sat, Jun 4, 2016 at 11:40 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
Thanks for helping me .
I could not solve the image render problem, I remove fedora 23 and
install it again but nothing has changed,
GMOD does not show any grid and could not render images.
When I want to run new human chr 2 and 22 project I saw following errors,
I don't know why?
-------------------- EXCEPTION -------------------- MSG: Access denied for
Bio::DB::SeqFeature::Store::DBI::mysql::init
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:217 STACK
Bio::DB::SeqFeature::Store::new
/usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:388 STACK (eval)
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44 STACK
Bio::Graphics::Browser2::DataBase::open_database
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44 STACK
Bio::Graphics::Browser2::DataSource::open_database
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997 STACK
Bio::Graphics::Browser2::Render::region
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1110 STACK
Bio::Graphics::Browser2::Render::segment
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1191 STACK
Bio::Graphics::Browser2::Render::_update_state
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1926 STACK
Bio::Graphics::Browser2::Render::update_state
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1916 STACK
Bio::Graphics::Browser2::Render::run
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:290 STACK toplevel
/var/www/cgi-bin/gb2/gbrowse:50 -------------------------------------------
I searched and changed number of issues but It seems there is no escape
from them.
How can I fix these problems?
Kind regards,
Ahmad

Post by Scott Cain
Hi Sayed,
This problem sounds very similar to another just posted to the mailing
http://gmod.827538.n3.nabble.com/GBrowse2-tracks-not-rendering-correctly-td4054457.html
Also, people have had issues with newer versions of apache (2.4)
http://gmod.827538.n3.nabble.com/gbrowse-problem-td4053878.html
Scott
On Wed, May 25, 2016 at 10:09 AM, Seyed Ahmad Mousavi <

Post by Seyed Ahmad Mousavi
Hi
I've installed gbrowse 2.54 on Fedora 23, but during working with human
sample chr 22 and chr2 the GBrowse does not show rulers and grids. You
could see my page I got from screen.
How can I fix the problem?
Kind regards,
--
Ahmad Mousavi
Royan Institute,
Tehran, Iran
------------------------------------------------------------------------------
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
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