can't locate method buttons_url - error for Gbrowse_syn

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

can't locate method buttons_url - error for Gbrowse_syn

Jayaraman, Pushkala


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/ 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.


GBrowse configuration files


Preinstalled sample database(s)


Online tutorial and sample data files


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.




Please help!

Is the error related to the paths?

Pushkala Jayaraman


Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229


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:
Gmod-gbrowse mailing list
[hidden email]