Where to Start

Those unfamiliar the Generic Genome Browser are encouraged to read the help files and the configuration guide. Those familiar with the original GMOD GBrowse application, and those that have a low patience for instruction manuals, are welcome to go straight to the following section for instructions on installing the sample configuration.

Using the Sample

To setup a Java GBrowse configuration, you will need access to a MySQL database and some basic knowledge of: administering MySQL, editing HTML, and using PERL scripts. Throughout this section, the following keywords will be in bold to indicate that they should be replaced with values specific to your configuration as indicated.

Keyword	Description
db_name	The name of the MySQL database, that will hold the genome data.
mysql_database_url	The URL for the desired MySQL database. For example: mysql://your.domain.edu/db_name.
path_to_GFF_file	The paths to the sample GFF files. For example: ~/Java_GBrowse_0.9.9/Sample/volvox_final.conf.
secure_db_user_name	The user name that Java GBrowse should use to access the MySQL database. It is recommended that you create a user account with select-only (read-only) privileges for security reasons.
secure_db_password	The password for the user secure_db_user_name.

1) Create the database

Within MySQL, create two empty databases to hold the data to be browsed (the GFF files will be imported into these databases). It is also recommended that you create a select-only (read-only) user login for each database to be used in the corresponding configuration file. (For details, see Configuration section on "Creating MySQL database").

2) Install the Java GBrowse

Download the Java GBrowse zip file from the site http://agcol.arizona.edu/software/java_gbrowse/download/. Unzip the files in the web accessible directory under your webserver. (Click here to see Package Contents below.)
Note: Due to the security restrictions placed on applets, the Java GBrowse must be served from the same host IP address as the MySQL database.

3) Import the data

To import the GFF files (rice_chr12.gff and volvox_all.gff in Sample folder) into MySQL you must first download and install the Bioperl package. Then to import each GFF file, use the following command:

bp_bulk_load_gff.pl -c -d mysql_database_url path_to_GFF_file

Note: The bp_bulk_load_gff.pl script is distributed with the bioperl package under scripts/Bio-DB-GFF/ folder.

4) Modify the configuration files

Open up the sample configuration files (volvox_final.conf and ricefpcchr.conf) and, where indicated at the top of the files, set the correct URL for the appropriate MySQL database.

[GENERAL]
db_args = user = pass =	-adaptor com.mysql.jdbc.Driver -dsn jdbc:mysql_database_url secure_db_user_name secure_db_password

5) Open the web page

Open the web page sample_web_page.htm under Sample folder using your web URL.

Note: Due to the security restrictions placed on applets, Java GBrowse will only work if the web page is opened remotely through a URL. (If it is opened from the local hard drive, the applet will not be allowed access to the host serving the MySQL database.)