Assist in GMOD

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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

------------------------------------------------------------------------------
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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Re: Assist in GMOD

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):


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


Scott


On Wed, May 25, 2016 at 10:09 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
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
[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: Assist in GMOD

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 <[hidden email]> wrote:
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 user 'apache'@'localhost' (using password: NO) STACK 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

On Wed, May 25, 2016 at 10:20 AM, Scott Cain <[hidden email]> wrote:
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):


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


Scott


On Wed, May 25, 2016 at 10:09 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
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
[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

------------------------------------------------------------------------------
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planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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