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
- $CGIBIN/gbrowse
- $CGIBIN/gbrowse_img
- $CGIBIN/gbrowse_details
- 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