   kent/browserbox/

This directory contains the config files that are needed for the 
Genome Browser in a box. It should be possible to convert
a Ubuntu 14 installation into a Genome Browser in a box by copying all these
files into the root directory as sudo. (Redmine #11957)

The main file that is changed 90% of the time when GBIB changes is this one:

   ~/kent/src/browserbox/root/updateBrowser.sh

It is the big script that is run on every start and also whenever the flag file
changes on hgdownload, after an hgdownload update (see the wiki documentation
below)

See the main gbib doc page:
http://genomewiki.ucsc.edu/genecats/index.php/Genome_Browser_in_a_Box_config

There are at least five wiki pages for every aspect of GBIB: development, 
configuration, updates, release process and pushes.

The following symlinks are not in git and have to be set manually :
usr/local/apache/htdocs/folders -> /media
usr/local/apache/trash ->  /data/trash/
usr/local/apache/userdata -> /data/userdata/
var/lib/mysql -> /data/mysql

Change ownerships of /data/gbdb, /data/trash and /data/userdata to www-data and /data/mysql to mysql

This tree does not include the trash cleaner binaries as they are > 5MB. Ask
Hiram to install the trash cleaner if you need it fixed or changed.

The directory clientInstall/ contains two small scripts that add the entry
"genome.ucsc.local" to the local hosts file. One is written in VisualBasic for
Windows, the other is in AppleScript for OSX. The AppleScript version also
contains a firewall rule that redirects localhost:1234 to localhost:80, the
only way to get a restricted port (<1024) to work with VirtualBox. 
(Redmine #12834)
The Applescript can be packaged into an app with the AppleScript editor. The
result can only be copied around as a zip file due to OSX special file
attributes.

the files packages-ubuntu*.txt are the lists of packages installed on the final
gbib in ubuntu13 and ubuntu14.

Various changes of the box are documented in root/changes.txt

The red box clipart is from http://www.clker.com/clipart-14656.html


