gbrowse_syn: no second species is displayed

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gbrowse_syn: no second species is displayed

sunnyjoy
Hi All,
I am a user of Gbrowse2 for almost three years so I am giving gbrowse_syn a try for my second genome.  I updated my Gbrowse (v 2.04) to v2.52 (OS: Ubuntu 12.04) and everything on Gbrowse worked fine. When I followed the tutorial of gbrowse_syn. loading alignment result to mysql and rename configure file works fine. However, I couldn't  get the same alignment image as I clicked the example link. There are a couple of things are unusual.
1.No track is displayed when I click two  example links. But change the coordinates to right half of the chromosome (eg.3:1352001..1659200 ) display one genome and mapped genes. But no second genome is ever displayed.
2. Under  gbrowse_syn, I can NOT use mouse to select or drag a region to zoom in or out in overview panel . Under gbrowse, it works just fine.

No error information is displayed on gbrowse,
in apache error log, I had two errors,
1. File does not exist /var/www/gbrowse2/js/toggle.js.  I couldn't not find the file in that directory. After a google search, someone suggest uses toggle.js from old gbrowse. So I downloaded the toggle.js file from gbrowse1.x and copied the file to /var/www/gbrowse2/js/. Now the error massage disappears but I still can not use mouse on overview panel. 

2. Use of uninitialized value $rest[1] error. It happens everything I changed the coordinates. Switching from memory adapter to Mysql adapter does not solve the problem.
[Thu Oct 04 16:05:45 2012] [error] [client 127.0.0.1] [Thu Oct  4 16:05:45 2012] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at (eval 130) line 15., referer: http://localhost/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=wild_rice;name=3:1..400000

Any suggestion will be appreciated. Thank you.

Yingjia Shen
Texas State University





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Re: gbrowse_syn: no second species is displayed

Sheldon McKay
Hi  Shen Yingjia,

Thanks for your message. It looks like a few things have gotten out of
synch with gbrowse_syn and Gbrowse 2.  I will let you know when this
is sorted out.

Sheldon

Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
(516) 367-5185
www.dnalc.org


On Thu, Oct 4, 2012 at 5:41 PM, Shen Yingjia <[hidden email]> wrote:

> Hi All,
> I am a user of Gbrowse2 for almost three years so I am giving gbrowse_syn a
> try for my second genome.  I updated my Gbrowse (v 2.04) to v2.52 (OS:
> Ubuntu 12.04) and everything on Gbrowse worked fine. When I followed the
> tutorial of gbrowse_syn. loading alignment result to mysql and rename
> configure file works fine. However, I couldn't  get the same alignment image
> as I clicked the example link. There are a couple of things are unusual.
> 1.No track is displayed when I click two  example links. But change the
> coordinates to right half of the chromosome (eg.3:1352001..1659200 ) display
> one genome and mapped genes. But no second genome is ever displayed.
> 2. Under  gbrowse_syn, I can NOT use mouse to select or drag a region to
> zoom in or out in overview panel . Under gbrowse, it works just fine.
>
> No error information is displayed on gbrowse,
> in apache error log, I had two errors,
> 1. File does not exist /var/www/gbrowse2/js/toggle.js.  I couldn't not find
> the file in that directory. After a google search, someone suggest uses
> toggle.js from old gbrowse. So I downloaded the toggle.js file from
> gbrowse1.x and copied the file to /var/www/gbrowse2/js/. Now the error
> massage disappears but I still can not use mouse on overview panel.
>
> 2. Use of uninitialized value $rest[1] error. It happens everything I
> changed the coordinates. Switching from memory adapter to Mysql adapter does
> not solve the problem.
> [Thu Oct 04 16:05:45 2012] [error] [client 127.0.0.1] [Thu Oct  4 16:05:45
> 2012] gbrowse_syn: Use of uninitialized value $rest[1] in join or string at
> (eval 130) line 15., referer:
> http://localhost/cgi-bin/gb2/gbrowse_syn/oryza/?search_src=wild_rice;name=3:1..400000
>
> Any suggestion will be appreciated. Thank you.
>
> Yingjia Shen
> Texas State University
>
>
>
>
>
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> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
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> Gmod-gbrowse mailing list
> [hidden email]
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>

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Re: gbrowse_syn: no second species is displayed

Riccardo Rinaldi
Hello everybody,
I'm a new user of Gbrowse2, v2.55. I followed the Gbrowse tutorial with the
volvox and C. elegans exemples and everything was fine. Then, as Shen
Yingjia, I tried the tutorial with Gbrowse_syn, but I had some troubles very
similar to those explained in this thread.

First of all I cannot get the same alignment image as I clicked the example
link. The image is blocked, I can't get any zoom and I can't move on the
sequence with the mouse commands.  Contrary to Shen Yingjia, I haven't any
genome image when I set 3:1352001..1659200 coordinates.
this is the image I get after clicking on the first exemple:

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712489/02.png>

The error I get on apache2 error.log are the same of Shen Yingjia. I
resolved the first one downloading from the internet the toggle.js file in
the js directory.
I continue though to get this error:
[Tue Apr 22 04:59:46 2014] [error] [client 127.0.0.1] [Tue Apr 22 04:59:46
2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at
/usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143.
I though there was something wrong in the config files, but I didn't changed
nothing from those given by the developers.

I'm really interested to know what kind of arrangement you suggested for
resolve this problem.

Thank you,
Riccardo



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Re: gbrowse_syn: no second species is displayed

Sheldon McKay
Hi Riccardo,

The bugs associated with GBrowse 2.55 (CPAN) are resolved on the github repository for GBrowse.  To update from github:

$ cd GBrowse
$ perl Build.PL
$ sudo ./Build install

Please let me know if this does not resolve your issues.

Sheldon McKay



On Tue, Apr 22, 2014 at 3:11 PM, Riccardo_Rinaldi <[hidden email]> wrote:
Hello everybody,
I'm a new user of Gbrowse2, v2.55. I followed the Gbrowse tutorial with the
volvox and C. elegans exemples and everything was fine. Then, as Shen
Yingjia, I tried the tutorial with Gbrowse_syn, but I had some troubles very
similar to those explained in this thread.

First of all I cannot get the same alignment image as I clicked the example
link. The image is blocked, I can't get any zoom and I can't move on the
sequence with the mouse commands.  Contrary to Shen Yingjia, I haven't any
genome image when I set 3:1352001..1659200 coordinates.
this is the image I get after clicking on the first exemple:

<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712489/02.png>

The error I get on apache2 error.log are the same of Shen Yingjia. I
resolved the first one downloading from the internet the toggle.js file in
the js directory.
I continue though to get this error:
[Tue Apr 22 04:59:46 2014] [error] [client 127.0.0.1] [Tue Apr 22 04:59:46
2014] gbrowse_syn: Use of uninitialized value $_[1] in hash element at
/usr/local/share/perl/5.14.2/Bio/Graphics/FeatureFile.pm line 1143.
I though there was something wrong in the config files, but I didn't changed
nothing from those given by the developers.

I'm really interested to know what kind of arrangement you suggested for
resolve this problem.

Thank you,
Riccardo



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Re: gbrowse_syn: no second species is displayed

Riccardo Rinaldi
Hello Sheldon,
thanks for your help.

I updated my Gbrowse as you suggested. Unfortunately gbrowse_syn continue to
have problem. Now is the perl script to bear some error. This is from my
Apache error.log:
[error] [client 127.0.0.1] [Thu May  1 10:27:12 2014] gbrowse_syn: Use of
uninitialized value $ENV{"GBROWSE_CONF"} in concatenation (.) or string at
/usr/lib/cgi-bin/gbrowse_syn line 9.

Riccardo




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Re: gbrowse_syn: no second species is displayed

Sheldon McKay
Hi Riccardo,

That environmental variable is usually set by Apache.  Please do a fresh git pull to get the fix for this problem.

Sheldon




On Thu, May 1, 2014 at 8:35 PM, Riccardo Rinaldi <[hidden email]> wrote:
Hello Sheldon,
thanks for your help.

I updated my Gbrowse as you suggested. Unfortunately gbrowse_syn continue to
have problem. Now is the perl script to bear some error. This is from my
Apache error.log:
[error] [client 127.0.0.1] [Thu May  1 10:27:12 2014] gbrowse_syn: Use of
uninitialized value $ENV{"GBROWSE_CONF"} in concatenation (.) or string at
/usr/lib/cgi-bin/gbrowse_syn line 9.

Riccardo




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Re: gbrowse_syn: no second species is displayed

Riccardo Rinaldi
Hi Sheldon,
thank you for the help, now Gbrowse_syn is working.

Thank you,
Riccardo



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