Generic Genome Browser, v2

Welcome to the Generic Genome Browser!

Example Database

Example in-memory databases from yeast chromosomes 1 and 2 have been installed for you. Try it at this URL:

/cgi-bin/gb2/gbrowse/yeast (simple example) /cgi-bin/gb2/gbrowse/yeast_advanced (advanced example) /cgi-bin/gb2/gbrowse/yeast_renderfarm (renderfarm example)

The "renderfarm" example will only work if a local gbrowse_slave render slave daemon is running. To launch the daemon, run this command as the root user:

% /etc/init.d/gbrowse-slave start

If you allowed the install process to adjust your Apache configuration, you can use the alias /gb2 as an alternative to /cgi-bin/gb2:

/gb2/gbrowse/yeast /gb2/gbrowse/yeast_advanced /gb2/gbrowse/yeast_renderfarm

Directory Paths

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

GBrowse documentation, stylesheets and in-memory databases.
$HTDOCS

GBrowse configuration files
$CONF/GBrowse.conf

Preinstalled sample database(s)
$DATABASES

Online tutorial and sample data files
$HTDOCS/tutorial.

GBrowse CGI (web) scripts

Installation and configuration manual
GBrowse 2.0 HOWTO

Temporary directories for cached images and sessions.
$TMP

Miscellaneous documentation and READMEs
$HTDOCS/docs/pod/MAKE_IMAGES_HOWTO.html gives directions for creating stand-alone pictures with the gbrowse_img script (at http://localhost/gbrowse2/docs/pod/MAKE_IMAGES_HOWTO.html).

$HTDOCS/docs/pod/README-gff-files.html describes methods for obtaining GBrowse compatible GFF files from WormBase, FlyBase, SGD and NCBI/human (at http://localhost/gbrowse2/docs/pod/README-gff-files.html).

$HTDOCS/docs/pod/PLUGINS_HOWTO.html gives directions for creating plugins (at http://localhost/gbrowse2/docs/pod/PLUGINS_HOWTO.html).

$HTDOCS/docs/pod/README-chado.html gives notes for using GBrowse with chado (at http://localhost/gbrowse2/docs/pod/README-chado.html).

$HTDOCS/docs/pod/DAS_HOWTO.html gives notes for using GBrowse as a Distributed Annotation System (DAS) server and client (at http://localhost/gbrowse2/docs/pod/DAS_HOWTO.html).

$HTDOCS/docs/pod/ORACLE_AND_POSTGRESQL.html gives notes for running GBrowse on top of Oracle and PostgreSQL database servers (at http://localhost/gbrowse2/docs/pod/ORACLE_AND_POSTGRESQL.html).

$HTDOCS/docs/pod/BIOSQL_ADAPTER_HOWTO.html has instructions for running GBrowse on top of a BioSQL database (at http://localhost/gbrowse2/docs/pod/BIOSQL_ADAPTER_HOWTO.html).

$HTDOCS/docs/pod/GENBANK_HOWTO.html has notes for loading and browsing GenBank formated files (at http://localhost/gbrowse2/docs/pod/GENBANK_HOWTO.html).

$HTDOCS/docs/pod/INSTALL.MacOSX.html has notes for installing GBrowse on MacOSX (at http://localhost/gbrowse2/docs/pod/INSTALL.MacOSX.html).

Learning More

To find out more about Gbrowse, try the:


Lincoln D. Stein, lstein@cshl.org
Cold Spring Harbor Laboratory
Last modified: Wed Nov 12 18:13:40 EST 2008