Re: can't locate method buttons_url - error forGbrowse_syn

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Re: can't locate method buttons_url - error forGbrowse_syn

Sheldon McKay
Hi Pushkala,

This should be fixed if you do an svn update to the source code.

Sheldon


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Mon, Jun 7, 2010 at 7:32 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,
>
> I came across a possible bug in the Gbrowse_syn code. Please read below:
>
>
>
>
>
> Hello,
>
> I managed to get the page visible..
>
> Minor change in the .synconf –dsn argument
>
> Join = dbi:mysql:database=DBNAME;host=HOST;user=USRNAME;password=PASSWD
>
>
>
> The argument for password is ‘password’ and not ‘pass’ (the gbrowse2 conf
> files use ‘pass’ as argument)
>
>
>
> But the –dsn argument in the individual data source .conf files remains
> similar to the datasource.conf files for gbrowse2
>
>
>
>
>
> I now seem to get other errors when I try and click on the example data
> source:
>
> Software error:
>
> Can't locate object method "buttons_url" via package
> "Bio::Graphics::Browser2" at
> /usr/local/perl5.8.9/lib/site_perl/5.8.9/x86_64-linux/Legacy/Graphics/Browser/Util.pm
> line 163.
>
> For help, please send mail to the webmaster ([hidden email]), giving this
> error message and the time and date of the error.
>
> This error corresponds to this line:
>
> push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||
> '/gbrowse2/images/buttons');
>
>
>
> the folder /images/buttons exists and I have given it full privileges..
>  Here are my data file paths and configuration file paths:
>
> Data Files
>
> The oryza data source contains genome annotations in GFF3 flat files for two
> rice species and blastz-derived whole genome aligment data between the two
> species.
>
> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/rice/rice.gff3
> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/wild_rice/wild_rice.gff3
> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/alignments/rice.aln
>
> Configuration files
>
> Configuration files for the two species can be found at the locations below.
> The oryza.synconf file is disabled pending installation of the joining
> database. rice_synteny.conf and wild_rice_synteny.conf are the configuration
> files for the individual species. They are already set up to use the
> in-memory adapter and the GFF3 flat files listed above.
>
> /usr/local/gbrowse2/etc/synteny/oryza.synconf.disabled
> /usr/local/gbrowse2/etc/synteny/rice_synteny.conf
> /usr/local/gbrowse2/etc/synteny/wild_rice_synteny.conf
>
>
>
>
>
> Here are the paths for Gbrowse2 :
>
> Directory Paths
>
> For future reference, here is where you've installed GBrowse's various
> components:
>
> GBrowse documentation, stylesheets and in-memory databases.
>
> /usr/local/gbrowse2/htdocs
>
> GBrowse configuration files
>
> /usr/local/gbrowse2/etc/GBrowse.conf
>
> Preinstalled sample database(s)
>
> /usr/local/gbrowse2/databases
>
> Online tutorial and sample data files
>
> /usr/local/gbrowse2/htdocs/tutorial.
>
> GBrowse CGI (web) scripts
>
> ·         /usr/local/apache3/cgi-bin/gbrowse
>
> ·         /usr/local/apache3/cgi-bin/gbrowse_img
>
> ·         /usr/local/apache3/cgi-bin/gbrowse_details
>
> Installation and configuration manual
>
> GBrowse 2.0 HOWTO
>
> Temporary directories for cached images and sessions.
>
> /usr/local/gbrowse2/tmp
>
>
>
>
>
> I went ahead and checked the perl module Util.pm under line 163 and I found
> this:
>
> push @args,(-lang=>($CONFIG->language_code)[0]) if $CONFIG->language_code;
>
>   push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||
> '/gbrowse2/images/buttons');
>
>   push @args,(-gbrowse_js     => $CONFIG->globals->js_url      ||
> '/gbrowse2/js');
>
>   push @args,(-reset_toggle   => 1)               if $reset_all;
>
>
>
> The underlined line is the problem area.. although the folder buttons is in
> the path /gbrowse2/images/buttons
>
> Please help!
>
> Is the error related to the paths?
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: can't locate method buttons_url - error forGbrowse_syn

Jayaraman, Pushkala

Hi Sheldon,

Thanks for the patch. I am now able to see the synteny. Although, I am not able to get the scale for the rubber-band dragging. I am not able to see that.

 

 

The error logs point to:

[Mon Jun 07 17:48:00 2010] [error] [client 141.106.161.52] [Mon Jun  7 17:48:00 2010] gbrowse_syn: Use of uninitialized value in join or string at (eval 132) line 15., referer: http://hastings.hmgc.mcw.edu:83/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:16050173..16064974

 

Do let me know where I am going wrong…

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Monday, June 07, 2010 11:27 AM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

 

This should be fixed if you do an svn update to the source code.

 

Sheldon

 

 

Sheldon McKay, PhD

Scientific Lead, iPlant Collaborative

BIO5 Institute, University of Arizona

Email: [hidden email]

Google Voice:  (203) 701-9204

 

 

 

On Mon, Jun 7, 2010 at 7:32 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,

> 

> I came across a possible bug in the Gbrowse_syn code. Please read below:

> 

> 

> 

> 

> 

> Hello,

> 

> I managed to get the page visible..

> 

> Minor change in the .synconf –dsn argument

> 

> Join = dbi:mysql:database=DBNAME;host=HOST;user=USRNAME;password=PASSWD

> 

> 

> 

> The argument for password is ‘password’ and not ‘pass’ (the gbrowse2 conf

> files use ‘pass’ as argument)

> 

> 

> 

> But the –dsn argument in the individual data source .conf files remains

> similar to the datasource.conf files for gbrowse2

> 

> 

> 

> 

> 

> I now seem to get other errors when I try and click on the example data

> source:

> 

> Software error:

> 

> Can't locate object method "buttons_url" via package

> "Bio::Graphics::Browser2" at

> /usr/local/perl5.8.9/lib/site_perl/5.8.9/x86_64-linux/Legacy/Graphics/Browser/Util.pm

> line 163.

> 

> For help, please send mail to the webmaster ([hidden email]), giving this

> error message and the time and date of the error.

> 

> This error corresponds to this line:

> 

> push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

> 

> 

> 

> the folder /images/buttons exists and I have given it full privileges..

>  Here are my data file paths and configuration file paths:

> 

> Data Files

> 

> The oryza data source contains genome annotations in GFF3 flat files for two

> rice species and blastz-derived whole genome aligment data between the two

> species.

> 

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/rice/rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/wild_rice/wild_rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/alignments/rice.aln

> 

> Configuration files

> 

> Configuration files for the two species can be found at the locations below.

> The oryza.synconf file is disabled pending installation of the joining

> database. rice_synteny.conf and wild_rice_synteny.conf are the configuration

> files for the individual species. They are already set up to use the

> in-memory adapter and the GFF3 flat files listed above.

> 

> /usr/local/gbrowse2/etc/synteny/oryza.synconf.disabled

> /usr/local/gbrowse2/etc/synteny/rice_synteny.conf

> /usr/local/gbrowse2/etc/synteny/wild_rice_synteny.conf

> 

> 

> 

> 

> 

> Here are the paths for Gbrowse2 :

> 

> Directory Paths

> 

> For future reference, here is where you've installed GBrowse's various

> components:

> 

> GBrowse documentation, stylesheets and in-memory databases.

> 

> /usr/local/gbrowse2/htdocs

> 

> GBrowse configuration files

> 

> /usr/local/gbrowse2/etc/GBrowse.conf

> 

> Preinstalled sample database(s)

> 

> /usr/local/gbrowse2/databases

> 

> Online tutorial and sample data files

> 

> /usr/local/gbrowse2/htdocs/tutorial.

> 

> GBrowse CGI (web) scripts

> 

> ·         /usr/local/apache3/cgi-bin/gbrowse

> 

> ·         /usr/local/apache3/cgi-bin/gbrowse_img

> 

> ·         /usr/local/apache3/cgi-bin/gbrowse_details

> 

> Installation and configuration manual

> 

> GBrowse 2.0 HOWTO

> 

> Temporary directories for cached images and sessions.

> 

> /usr/local/gbrowse2/tmp

> 

> 

> 

> 

> 

> I went ahead and checked the perl module Util.pm under line 163 and I found

> this:

> 

> push @args,(-lang=>($CONFIG->language_code)[0]) if $CONFIG->language_code;

> 

>   push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

> 

>   push @args,(-gbrowse_js     => $CONFIG->globals->js_url      ||

> '/gbrowse2/js');

> 

>   push @args,(-reset_toggle   => 1)               if $reset_all;

> 

> 

> 

> The underlined line is the problem area.. although the folder buttons is in

> the path /gbrowse2/images/buttons

> 

> Please help!

> 

> Is the error related to the paths?

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email]

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu

> 

> 

> 

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo

> 


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: can't locate method buttons_url - error forGbrowse_syn

Sheldon McKay
Hi Pushkala,

Do you mean you can not see the overview panel or that rubber band selection is not working?  Are there are any error messages in the javascript console?  Is it possible for you to put your implementation on an open port so I can see for myself?

Sheldon


On Mon, Jun 7, 2010 at 3:50 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hi Sheldon,

Thanks for the patch. I am now able to see the synteny. Although, I am not able to get the scale for the rubber-band dragging. I am not able to see that.

 

 

The error logs point to:

[Mon Jun 07 17:48:00 2010] [error] [client 141.106.161.52] [Mon Jun  7 17:48:00 2010] gbrowse_syn: Use of uninitialized value in join or string at (eval 132) line 15., referer: http://hastings.hmgc.mcw.edu:83/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:16050173..16064974

 

Do let me know where I am going wrong…

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Monday, June 07, 2010 11:27 AM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

 

This should be fixed if you do an svn update to the source code.

 

Sheldon

 

 

Sheldon McKay, PhD

Scientific Lead, iPlant Collaborative

BIO5 Institute, University of Arizona

Email: [hidden email]

Google Voice:  (203) 701-9204

 

 

 

On Mon, Jun 7, 2010 at 7:32 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,

> I came across a possible bug in the Gbrowse_syn code. Please read below:

> Hello,

> I managed to get the page visible..

> Minor change in the .synconf –dsn argument

> Join = dbi:mysql:database=DBNAME;host=HOST;user=USRNAME;password=PASSWD

> The argument for password is ‘password’ and not ‘pass’ (the gbrowse2 conf

> files use ‘pass’ as argument)

> But the –dsn argument in the individual data source .conf files remains

> similar to the datasource.conf files for gbrowse2

> I now seem to get other errors when I try and click on the example data

> source:

> Software error:

> Can't locate object method "buttons_url" via package

> "Bio::Graphics::Browser2" at

> /usr/local/perl5.8.9/lib/site_perl/5.8.9/x86_64-linux/Legacy/Graphics/Browser/Util.pm

> line 163.

> For help, please send mail to the webmaster ([hidden email]), giving this

> error message and the time and date of the error.

> This error corresponds to this line:

> push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

> the folder /images/buttons exists and I have given it full privileges..

>  Here are my data file paths and configuration file paths:

> Data Files

> The oryza data source contains genome annotations in GFF3 flat files for two

> rice species and blastz-derived whole genome aligment data between the two

> species.

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/rice/rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/wild_rice/wild_rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/alignments/rice.aln

> Configuration files

> Configuration files for the two species can be found at the locations below.

> The oryza.synconf file is disabled pending installation of the joining

> database. rice_synteny.conf and wild_rice_synteny.conf are the configuration

> files for the individual species. They are already set up to use the

> in-memory adapter and the GFF3 flat files listed above.

> /usr/local/gbrowse2/etc/synteny/oryza.synconf.disabled

> /usr/local/gbrowse2/etc/synteny/rice_synteny.conf

> /usr/local/gbrowse2/etc/synteny/wild_rice_synteny.conf

> Here are the paths for Gbrowse2 :

> Directory Paths

> For future reference, here is where you've installed GBrowse's various

> components:

> GBrowse documentation, stylesheets and in-memory databases.

> /usr/local/gbrowse2/htdocs

> GBrowse configuration files

> /usr/local/gbrowse2/etc/GBrowse.conf

> Preinstalled sample database(s)

> /usr/local/gbrowse2/databases

> Online tutorial and sample data files

> /usr/local/gbrowse2/htdocs/tutorial.

> GBrowse CGI (web) scripts

> ·         /usr/local/apache3/cgi-bin/gbrowse

> ·         /usr/local/apache3/cgi-bin/gbrowse_img

> ·         /usr/local/apache3/cgi-bin/gbrowse_details

> Installation and configuration manual

> GBrowse 2.0 HOWTO

> Temporary directories for cached images and sessions.

> /usr/local/gbrowse2/tmp

> I went ahead and checked the perl module Util.pm under line 163 and I found

> this:

> push @args,(-lang=>($CONFIG->language_code)[0]) if $CONFIG->language_code;

>   push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

>   push @args,(-gbrowse_js     => $CONFIG->globals->js_url      ||

> '/gbrowse2/js');

>   push @args,(-reset_toggle   => 1)               if $reset_all;

> The underlined line is the problem area.. although the folder buttons is in

> the path /gbrowse2/images/buttons

> Please help!

> Is the error related to the paths?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: can't locate method buttons_url - error forGbrowse_syn

Jayaraman, Pushkala

 

Hi Sheldon,

As you see above on the left screen, the area under “Reference genome=Wild Rice” is blank. But as you can see below,  I am able to use the rubber Band selection over an invisible panel.. the scale has gone missing.. It shows the image like this on IExplorer and on Chrome. Whereas on FireFox, the RubberBand selection also does not work(see below for FireFox image)

 

 

As you can see, in FireFox, the panel is too small to allow any selection.. the scale is invisible here as well..

 

 

I am not sure if we can open any ports… But I can find out.. Do let me know in case you need any information regarding paths/config files etc...

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Sheldon McKay [mailto:[hidden email]]
Sent: Tuesday, June 08, 2010 9:28 AM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

Do you mean you can not see the overview panel or that rubber band selection is not working?  Are there are any error messages in the javascript console?  Is it possible for you to put your implementation on an open port so I can see for myself?

Sheldon

On Mon, Jun 7, 2010 at 3:50 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hi Sheldon,

Thanks for the patch. I am now able to see the synteny. Although, I am not able to get the scale for the rubber-band dragging. I am not able to see that.

 

 

The error logs point to:

[Mon Jun 07 17:48:00 2010] [error] [client 141.106.161.52] [Mon Jun  7 17:48:00 2010] gbrowse_syn: Use of uninitialized value in join or string at (eval 132) line 15., referer: http://hastings.hmgc.mcw.edu:83/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:16050173..16064974

 

Do let me know where I am going wrong…

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Monday, June 07, 2010 11:27 AM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

 

This should be fixed if you do an svn update to the source code.

 

Sheldon

 

 

Sheldon McKay, PhD

Scientific Lead, iPlant Collaborative

BIO5 Institute, University of Arizona

Email: [hidden email]

Google Voice:  (203) 701-9204

 

 

 

On Mon, Jun 7, 2010 at 7:32 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,

> I came across a possible bug in the Gbrowse_syn code. Please read below:

> Hello,

> I managed to get the page visible..

> Minor change in the .synconf –dsn argument

> Join = dbi:mysql:database=DBNAME;host=HOST;user=USRNAME;password=PASSWD

> The argument for password is ‘password’ and not ‘pass’ (the gbrowse2 conf

> files use ‘pass’ as argument)

> But the –dsn argument in the individual data source .conf files remains

> similar to the datasource.conf files for gbrowse2

> I now seem to get other errors when I try and click on the example data

> source:

> Software error:

> Can't locate object method "buttons_url" via package

> "Bio::Graphics::Browser2" at

> /usr/local/perl5.8.9/lib/site_perl/5.8.9/x86_64-linux/Legacy/Graphics/Browser/Util.pm

> line 163.

> For help, please send mail to the webmaster ([hidden email]), giving this

> error message and the time and date of the error.

> This error corresponds to this line:

> push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

> the folder /images/buttons exists and I have given it full privileges..

>  Here are my data file paths and configuration file paths:

> Data Files

> The oryza data source contains genome annotations in GFF3 flat files for two

> rice species and blastz-derived whole genome aligment data between the two

> species.

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/rice/rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/wild_rice/wild_rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/alignments/rice.aln

> Configuration files

> Configuration files for the two species can be found at the locations below.

> The oryza.synconf file is disabled pending installation of the joining

> database. rice_synteny.conf and wild_rice_synteny.conf are the configuration

> files for the individual species. They are already set up to use the

> in-memory adapter and the GFF3 flat files listed above.

> /usr/local/gbrowse2/etc/synteny/oryza.synconf.disabled

> /usr/local/gbrowse2/etc/synteny/rice_synteny.conf

> /usr/local/gbrowse2/etc/synteny/wild_rice_synteny.conf

> Here are the paths for Gbrowse2 :

> Directory Paths

> For future reference, here is where you've installed GBrowse's various

> components:

> GBrowse documentation, stylesheets and in-memory databases.

> /usr/local/gbrowse2/htdocs

> GBrowse configuration files

> /usr/local/gbrowse2/etc/GBrowse.conf

> Preinstalled sample database(s)

> /usr/local/gbrowse2/databases

> Online tutorial and sample data files

> /usr/local/gbrowse2/htdocs/tutorial.

> GBrowse CGI (web) scripts

> ·         /usr/local/apache3/cgi-bin/gbrowse

> ·         /usr/local/apache3/cgi-bin/gbrowse_img

> ·         /usr/local/apache3/cgi-bin/gbrowse_details

> Installation and configuration manual

> GBrowse 2.0 HOWTO

> Temporary directories for cached images and sessions.

> /usr/local/gbrowse2/tmp

> I went ahead and checked the perl module Util.pm under line 163 and I found

> this:

> push @args,(-lang=>($CONFIG->language_code)[0]) if $CONFIG->language_code;

>   push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

>   push @args,(-gbrowse_js     => $CONFIG->globals->js_url      ||

> '/gbrowse2/js');

>   push @args,(-reset_toggle   => 1)               if $reset_all;

> The underlined line is the problem area.. although the folder buttons is in

> the path /gbrowse2/images/buttons

> Please help!

> Is the error related to the paths?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo

 


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Re: can't locate method buttons_url - error forGbrowse_syn

Sheldon McKay
Hi Pushkala,

Could you send along your config files.  Also, could you try running your browser with javascript turned off to see if the overview image is restored.  Also, any debugging info from the javascript console, firebug, the microsoft script debugger,  may be helpful.   In FireFox, you can see javascript errors in Tools->Error Console.

Sheldon


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204


On Tue, Jun 8, 2010 at 7:41 AM, Jayaraman, Pushkala <[hidden email]> wrote:

 

Hi Sheldon,

As you see above on the left screen, the area under “Reference genome=Wild Rice” is blank. But as you can see below,  I am able to use the rubber Band selection over an invisible panel.. the scale has gone missing.. It shows the image like this on IExplorer and on Chrome. Whereas on FireFox, the RubberBand selection also does not work(see below for FireFox image)

 

 

As you can see, in FireFox, the panel is too small to allow any selection.. the scale is invisible here as well..

 

 

I am not sure if we can open any ports… But I can find out.. Do let me know in case you need any information regarding paths/config files etc...

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Sheldon McKay [mailto:[hidden email]]
Sent: Tuesday, June 08, 2010 9:28 AM


To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

Do you mean you can not see the overview panel or that rubber band selection is not working?  Are there are any error messages in the javascript console?  Is it possible for you to put your implementation on an open port so I can see for myself?

Sheldon

On Mon, Jun 7, 2010 at 3:50 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hi Sheldon,

Thanks for the patch. I am now able to see the synteny. Although, I am not able to get the scale for the rubber-band dragging. I am not able to see that.

 

 

The error logs point to:

[Mon Jun 07 17:48:00 2010] [error] [client 141.106.161.52] [Mon Jun  7 17:48:00 2010] gbrowse_syn: Use of uninitialized value in join or string at (eval 132) line 15., referer: http://hastings.hmgc.mcw.edu:83/gb2/gbrowse_syn/oryza/?search_src=rice;name=3:16050173..16064974

 

Do let me know where I am going wrong…

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Monday, June 07, 2010 11:27 AM
To: Jayaraman, Pushkala
Cc: Gbrowse Mailing List
Subject: Re: can't locate method buttons_url - error forGbrowse_syn

 

Hi Pushkala,

 

This should be fixed if you do an svn update to the source code.

 

Sheldon

 

 

Sheldon McKay, PhD

Scientific Lead, iPlant Collaborative

BIO5 Institute, University of Arizona

Email: [hidden email]

Google Voice:  (203) 701-9204

 

 

 

On Mon, Jun 7, 2010 at 7:32 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello Sheldon,

> I came across a possible bug in the Gbrowse_syn code. Please read below:

> Hello,

> I managed to get the page visible..

> Minor change in the .synconf –dsn argument

> Join = dbi:mysql:database=DBNAME;host=HOST;user=USRNAME;password=PASSWD

> The argument for password is ‘password’ and not ‘pass’ (the gbrowse2 conf

> files use ‘pass’ as argument)

> But the –dsn argument in the individual data source .conf files remains

> similar to the datasource.conf files for gbrowse2

> I now seem to get other errors when I try and click on the example data

> source:

> Software error:

> Can't locate object method "buttons_url" via package

> "Bio::Graphics::Browser2" at

> /usr/local/perl5.8.9/lib/site_perl/5.8.9/x86_64-linux/Legacy/Graphics/Browser/Util.pm

> line 163.

> For help, please send mail to the webmaster ([hidden email]), giving this

> error message and the time and date of the error.

> This error corresponds to this line:

> push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

> the folder /images/buttons exists and I have given it full privileges..

>  Here are my data file paths and configuration file paths:

> Data Files

> The oryza data source contains genome annotations in GFF3 flat files for two

> rice species and blastz-derived whole genome aligment data between the two

> species.

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/rice/rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/wild_rice/wild_rice.gff3

> /usr/local/gbrowse2/htdocs/databases/gbrowse_syn/alignments/rice.aln

> Configuration files

> Configuration files for the two species can be found at the locations below.

> The oryza.synconf file is disabled pending installation of the joining

> database. rice_synteny.conf and wild_rice_synteny.conf are the configuration

> files for the individual species. They are already set up to use the

> in-memory adapter and the GFF3 flat files listed above.

> /usr/local/gbrowse2/etc/synteny/oryza.synconf.disabled

> /usr/local/gbrowse2/etc/synteny/rice_synteny.conf

> /usr/local/gbrowse2/etc/synteny/wild_rice_synteny.conf

> Here are the paths for Gbrowse2 :

> Directory Paths

> For future reference, here is where you've installed GBrowse's various

> components:

> GBrowse documentation, stylesheets and in-memory databases.

> /usr/local/gbrowse2/htdocs

> GBrowse configuration files

> /usr/local/gbrowse2/etc/GBrowse.conf

> Preinstalled sample database(s)

> /usr/local/gbrowse2/databases

> Online tutorial and sample data files

> /usr/local/gbrowse2/htdocs/tutorial.

> GBrowse CGI (web) scripts

> ·         /usr/local/apache3/cgi-bin/gbrowse

> ·         /usr/local/apache3/cgi-bin/gbrowse_img

> ·         /usr/local/apache3/cgi-bin/gbrowse_details

> Installation and configuration manual

> GBrowse 2.0 HOWTO

> Temporary directories for cached images and sessions.

> /usr/local/gbrowse2/tmp

> I went ahead and checked the perl module Util.pm under line 163 and I found

> this:

> push @args,(-lang=>($CONFIG->language_code)[0]) if $CONFIG->language_code;

>   push @args,(-gbrowse_images => $CONFIG->globals->buttons_url ||

> '/gbrowse2/images/buttons');

>   push @args,(-gbrowse_js     => $CONFIG->globals->js_url      ||

> '/gbrowse2/js');

>   push @args,(-reset_toggle   => 1)               if $reset_all;

> The underlined line is the problem area.. although the folder buttons is in

> the path /gbrowse2/images/buttons

> Please help!

> Is the error related to the paths?

> Pushkala Jayaraman

> Programmer/Analyst

> Rat Genome Database

> Human and Molecular Genetics Center

> Medical College of Wisconsin

> Email: [hidden email]

> Work: 414-955-2229

> www.rgd.mcw.edu

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo

 



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: can't locate method buttons_url - error forGbrowse_syn

m_sia
In reply to this post by Sheldon McKay

Hi.

I'm facing similar problem as Pushkala. I'm setting the rice database and I
received error
"Can't locate object method "buttons_url" via package
"Bio::Graphics::Browser2" at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Legacy/Graphics/Browser/Util.pm
line 163."

I'm using Gbrowse-2.07 on RHEL5 and I've reconfigure the directory path.

e.g. gbrowse data and image dic = /var/www/html/gbrowse2
gbrowse config = /etc/gbrowse2

I've run svn update from the gbrowse directory:
 $ svn update
Skipped '.'

Could anyone advise me on how I can get this to work?

Thank you



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Re: can't locate method buttons_url - errorforGbrowse_syn

Jayaraman, Pushkala
You need to change the method from button_url to buttons_url.. there was
a patch put out by Sheldon  a few months ago.. I didn't update Gbrowse,
I simply saw the latest change in Gbrowse_syn folder, compared that code
and the one we had and made the changes found by DIFF..

The only difference was that the button_url was changed to buttons_url..
in a method..

You should be able to find it :)



Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: msia [mailto:[hidden email]]
Sent: Wednesday, November 03, 2010 10:38 PM
To: [hidden email]
Subject: Re: [Gmod-gbrowse] can't locate method buttons_url -
errorforGbrowse_syn


Hi.

I'm facing similar problem as Pushkala. I'm setting the rice database
and I
received error
"Can't locate object method "buttons_url" via package
"Bio::Graphics::Browser2" at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Legacy/Graphi
cs/Browser/Util.pm
line 163."

I'm using Gbrowse-2.07 on RHEL5 and I've reconfigure the directory path.

e.g. gbrowse data and image dic = /var/www/html/gbrowse2
gbrowse config = /etc/gbrowse2

I've run svn update from the gbrowse directory:
 $ svn update
Skipped '.'

Could anyone advise me on how I can get this to work?

Thank you



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n-t-locate-method-buttons-url-error-forGbrowse-syn-tp458104p3249492.html
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David G. Thomson, author of the best-selling book "Blueprint to a
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business during the next growth cycle. Listen Now!
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Re: can't locate method buttons_url - errorforGbrowse_syn

m_sia
Hi...
could you lead me to the Gbrowse_syn folder which the changes need to be? So far, I've checked gbrowse_syn related folder in /etc and in the web folder and other gbrowse_syn.* but couldn't find the necessary changes.....
 
hope you can help!
 
thanks
msia


From: "Jayaraman, Pushkala" <[hidden email]>
To: msia <[hidden email]>; [hidden email]
Sent: Thu, November 4, 2010 9:31:22 PM
Subject: RE: [Gmod-gbrowse] can't locate method buttons_url - errorforGbrowse_syn

You need to change the method from button_url to buttons_url.. there was
a patch put out by Sheldon  a few months ago.. I didn't update Gbrowse,
I simply saw the latest change in Gbrowse_syn folder, compared that code
and the one we had and made the changes found by DIFF..

The only difference was that the button_url was changed to buttons_url..
in a method..

You should be able to find it :)



Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: msia [mailto:[hidden email]]
Sent: Wednesday, November 03, 2010 10:38 PM
To: [hidden email]
Subject: Re: [Gmod-gbrowse] can't locate method buttons_url -
errorforGbrowse_syn


Hi.

I'm facing similar problem as Pushkala. I'm setting the rice database
and I
received error
"Can't locate object method "buttons_url" via package
"Bio::Graphics::Browser2" at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Legacy/Graphi
cs/Browser/Util.pm
line 163."

I'm using Gbrowse-2.07 on RHEL5 and I've reconfigure the directory path.

e.g. gbrowse data and image dic = /var/www/html/gbrowse2
gbrowse config = /etc/gbrowse2

I've run svn update from the gbrowse directory:
$ svn update
Skipped '.'

Could anyone advise me on how I can get this to work?

Thank you



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n-t-locate-method-buttons-url-error-forGbrowse-syn-tp458104p3249492.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------
------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
_______________________________________________
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------------------------------------------------------------------------------
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David G. Thomson, author of the best-selling book "Blueprint to a
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business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
_______________________________________________
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