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:
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:
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.
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.
Here are the paths for Gbrowse2 :
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
Installation and configuration manual
Temporary directories for cached images and sessions.
Is the error related to the paths?
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
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