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.
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:
Lincoln D. Stein, lstein@cshl.org
Cold Spring Harbor Laboratory
Last modified: Thu Mar 18 18:59:16 PDT 2010