Generic Genome Browser, v2 (Cloud Image)

Welcome to the Generic Genome Browser (Cloud Image)!

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

Starter Databases

A series of starter databases have been preconfigured for you, consisting of:

• S. cerevisiae genome (April 11, sacCer3), Genes and DNA only
• S. cerevisiae, Chromosomes 1+2, (more tracks)
• S. cerevisiae, Chromosomes 1+2, (Chado database)
• C. elegans genome (WS220, ce10), Genes and DNA only
• H. sapiens genome (hg19, GRCh37), Genes and DNA only

You may add additional starter genomes at any time by running the command line script gbrowse_import_ucsc.pl and providing the UCSC Genome Browser build name:

 gbrowse_import_ucsc.pl mm10 'M. musculus genome (mm10, GRCm38)' 

Directory Paths

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

GBrowse documentation, stylesheets and in-memory databases.

/opt/gbrowse/htdocs

GBrowse configuration files

/opt/gbrowse/etc

Preinstalled sample database(s)

/opt/gbrowse/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.

/opt/gbrowse/tmp/gbrowse2

Learning More

To find out more about Gbrowse, try the:

• GBrowse 2.0 HOWTO
• GBrowse Tutorial