# Generic Genome Browser, v2, VirtualBox Edition

Welcome to the Generic Genome Browser, VirtualBox Edition!

## Documentation

Online tutorial and sample data files
  /var/www/gbrowse2/tutorial.
Installation and configuration manual
  GBrowse 2.0 HOWTO
Example scripts to control GBrowse from the command line
  /var/www/gbrowse2/example_scripts

## Example Databases

A few "starter" databases have been installed for you. You can access them from within the virtual machine at http://localhost/fgb2/gbrowse, or from outside the virtual machine using http://host.machine:8081/fgb2/gbrowse, where "host.machine" is the DNS name or IP address of the computer that is hosting VirtualBox.

- S. cerevisiae genome (April 2011), genes and DNA
- C. elegans genome (WS220), genes and DNA
- S. cerevisiae, advanced example (chromosomes 1+2 only)

More starter databases can be installed by running the command line script "gbrowse_import_ucsc_db.pl". Genome builds are selected using the UCSC genome browser build name. For example, to load the human genome: gbrowse_import_ucsc_db.pl hg19 'H. sapiens genome (hg19), genes and DNA'

## Directory Paths

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

GBrowse documentation, stylesheets and in-memory databases.
  /opt/gbrowse/var/www/gbrowse2

GBrowse configuration files
  /opt/gbrowse/etc

Preinstalled sample database(s)
  /opt/gbrowse/lib/gbrowse2/databases

GBrowse CGI (web) scripts
  - /usr/lib/cgi-bin/gb2/gbrowse
  - /usr/lib/cgi-bin/gb2/gbrowse_img
  - /usr/lib/cgi-bin/gb2/gbrowse_details

Temporary directories for cached images and sessions.
  /tmp/gbrowse2

## Learning More

To find out more about Gbrowse, try the:

- GBrowse 2.0 HOWTO
- GBrowse Tutorial

Last modified: Thu Mar 18 18:59:16 PDT 2010