Generic Genome Browser

# Generic Genome Browser, v2

Welcome to the Generic Genome Browser!

## 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

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

- http://your.host/cgi-bin/gb2/gbrowse/yeast (simple example)
- http://your.host/cgi-bin/gb2/gbrowse/yeast_advanced (advanced example)
- http://your.host/cgi-bin/gb2/gbrowse/yeast_renderfarm (yeast_renderfarm example)

The "yeast_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

### Alternative URLs

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

- http://your.host/gb2/gbrowse/yeast
- http://your.host/gb2/gbrowse/yeast_advanced
- http://your.host/gb2/gbrowse/yeast_renderfarm
- http://your.host/gb2/gbrowse/pop_demo (demo of embedded population allele frequency maps -- requires Template module to be installed)

### Accelerated Demos

If you have mod_fcgid, mod_fastcgi and/or ModPerl installed, you will have access to an accelerated version of gbrowse at these URLs:

- mod_fcgid
  - http://your.host/fgb2/gbrowse/yeast
  - http://your.host/fgb2/gbrowse/yeast_advanced
  - http://your.host/fgb2/gbrowse/yeast_renderfarm
- mod_fastcgi
  - http://your.host/fast/gbrowse/yeast
  - http://your.host/fast/gbrowse/yeast_advanced
  - http://your.host/fast/gbrowse/yeast_renderfarm
- mod_perl
  - http://your.host/mgb2/gbrowse/yeast
  - http://your.host/mgb2/gbrowse/yeast_advanced
  - http://your.host/mgb2/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

Preinstalled sample database(s)
  $DATABASES

GBrowse CGI (web) scripts
  - $CGIBIN/gbrowse
  - $CGIBIN/gbrowse_img
  - $CGIBIN/gbrowse_details

Temporary directories for cached images and sessions.
  $TMP

## 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