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Gbrowse on westgrid
GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. For more information about Gbrowse please visit:
Gbrowse is installed on one of westgrid web server called joffre. joffre is a web interface for bugaboo. The /home and /global/scratch directories of bugaboo are mounted on joffre. Due to security reason users can connect to joffre only through the web browser.
If you need to use Gbrowse please send your request to firstname.lastname@example.org to setup an account for you on joffre.
To run Gbrowse please go to the website
and click on "Gbrowse Users click here" where you will be able to login using your westgrid username and passwords. After login and before you run Gbrowse there is a web form that provides you the following:
- Create and modifying Gbrowse config files. You can create, modify or delete a Gbrowse configure file. Please note that in addition to this option you can create or edit a config file directly by going to ~/public_html/gbrowse/conf directory in bugaboo and edit your configure file. All configure file must have extension of .conf
- Run your Gbrowse. It runs your gbrowse. Default data source is "Yeast chromosomes 1 +2 (basic)" which comes as an example during account setup
- List of all users within your group. Upon your request you can make a group in which the members are able to view other members' configure files or even run others' Gbrowse. The group is totally independent of any other Linux groups that you might have created before. Please send your request to email@example.com if you are interested to have such group. Please note that members and sponsors should approve that request.
- view your log files. The log file is created by joffre web server and it provides users with some information about errors caused in providing the config files. This log file option is particularly design to diagnose the problem that user face up in preparing their config files.
Depending on how a configure file is written Gbrowse might needs to connect to a database. We support MySQL and PostgreSQL database software. Please take a look at MySQL and Postgres database softwares to find out about how to use them on westgrid.
For MySQL, in order to connect to mysql server using gbrowse the corresponding line in your gbrowse configure file should contains:
db_args = -adaptor DBI::mysql
-dsn [database name];mysql_read_default_file=/home/[username]/.my.cnf
where [username] is the corresponding user name and [database name] is the name of the database.