e1b3625f3a40bfee5c483284fa7f6b23bf6bd47d
max
  Tue Aug 21 13:18:40 2018 +0200
moving all config files in GBIB to the new .gi.ucsc.edu domain names
from the old .soe.ucsc.edu domain names. refs #21876
This commit only changes the versions of these files in the repo,
not the ones in the actual browserbox, as they still need to get
pushed into the browserbox, either by the pusing procedure from
hgdownload or by the build meister when he builds the GBIB VM image.
See
http://genomewiki.ucsc.edu/genecats/index.php/Gbib_release#Release_config_changes_to_GbIb
and the related pages in the genecats genomewiki.

diff --git src/browserbox/README.txt src/browserbox/README.txt
index 26512ef..2648d62 100644
--- src/browserbox/README.txt
+++ src/browserbox/README.txt
@@ -1,39 +1,63 @@
 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)
-
-See also the main gbib doc page:
+files into the root directory as sudo. (Redmine #11957) But we have 
+never done this, we have a running VM and don't need to rebuild it.
+
+The most important part of the GBIB setup is the update script, located in
+this directory under kent/browserbox/root/updateBrowser. Making changes to GBIB
+usually means changing this script as WE DO NOT MODIFY THE GBIB VM, we only
+make changes to the update script, so all running GBIBs out there will still
+work and they are all in sync.
+
+If you change the copy of the update script in this git repo, please be aware
+that it will not automatically land on GBIBs to prevent accidentally breaking
+them all. You change updateBrowser, copy it to hgwdev.gi.ucsc.edu/gbib, you
+test it on your own GBIB with "updateBrowser hgwdev". If it works, you commit the
+file into the git repo and request a push of the file from hgwdev.gi.ucsc.edu/gbib to
+hgdownload.gi.ucsc.edu/gbib. This is all explained in the genomewiki page below.
+
+This update script rsyncs the directory hgdownload::gbib/push whenever it updates
+into / so hg.conf updates, little binary tools or similar changes can also come
+in through the push directory. Again, we do not make changes to the GBIB VM, 
+but only through the update script or possibly through the push directory.
+
+PLEASE READ the main gbib doc page and the pages linked from there:
 http://genomewiki.ucsc.edu/genecats/index.php/Genome_Browser_in_a_Box_config
 
+---
+
+The following information is only relevant is you're thinking about rebuilding
+a GBIB-like system from this directory.
+
 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
+This tree here 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