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/root/hg.conf.offline src/browserbox/root/hg.conf.offline
index 8489518..d6ccfcb 100644
--- src/browserbox/root/hg.conf.offline
+++ src/browserbox/root/hg.conf.offline
@@ -1,28 +1,28 @@
 # special hg.conf for gbib with deactivated network access to UCSC
 
 # redirect /gbdb access to local directory first and fallback to UCSC
 # add the trailing slash
 gbdbLoc1=/data/gbdb/
-#gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/
+#gbdbLoc2=http://hgdownload.gi.ucsc.edu/gbdb/
 
 # read mysql data first from localhost and fallback to UCSC
 db.host=localhost
 db.user=root
 db.password=browser
 db.socket=/var/run/mysqld/mysqld.sock
-#slow-db.host=genome-mysql.soe.ucsc.edu
+#slow-db.host=genome-mysql.gi.ucsc.edu
 #slow-db.user=genomep
 #slow-db.password=password
 
 # use a table cache to speed up remote queries
 showTableCache=tableList
 
 # the rnaPlot binary is for the hgGene page
 rnaPlotPath=/usr/local/bin/RNAplot
 
 # galaxy and great cannot work from the box
 hgta.disableSendOutput=yes
 
 # redirect links to Encode PDF files back to UCSC
 hgEncodeVocabDocBaseUrl=http://genome.ucsc.edu
 
@@ -129,31 +129,31 @@
 
 # title of host of browser, this text be shown in the user interface of
 # the login/sign up screens
 login.browserName=Browser-in-a-Box
 # base url of browser installed
 login.browserAddr=http://127.0.0.1:1234
 # signature written at the bottom of hgLogin system emails
 login.mailSignature=None
 # from/return email address used for system emails
 login.mailReturnAddr=NOEMAIL
 
 # The following 6 parameters are used to set up your browser to accept user suggestions.
 # After a user submits a suggestion, both the user and the suggestion admin address below
 # will receive an email containing the suggestion.
 # email address for the suggestion admin
-#suggest.mailToAddr=suggestion@myuniversitysoe.edu
+#suggest.mailToAddr=suggestion@myuniversity.edu
 # sender address for the suggestion email 
 #suggest.mailFromAddr=browserAdministrator@mylab.university.edu
 # Keyword in the mail subject line to help filter out spam
 #suggest.filterKeyword=FORYOUREYESONLY
 ## signature written at the bottom of suggestion emails
 #suggest.mailSignature=My Lab browser administrator
 # contact address for suggestion follow up
 #suggest.mailReturnAddr=browserAdministrator@mylab.university.edu
 # browser name used in emails
 #suggest.browserName=myLab Genome Browser
 
 
 # The following instructions for using genomewiki has been replaced by the 
 # new hgLogin function as describe above. The section are preserved here
 # to serve as a reference for the current mirror site using locally
@@ -169,31 +169,31 @@
 #	The example here is for $wgDBName=wikidb and $wgDBprefix=mw1
 # wiki.host=genomewiki.ucsc.edu
 # wiki.userNameCookie=wikidb_mw1_UserName
 # wiki.loggedInCookie=wikidb_mw1_UserID
 #	You will need to create the namedSessionDb table in your hgcentral db:
 #	hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql
 #  See notes about this in the source tree: src/hg/wikiMods/
 
 # wikiTrack function turned on 2009 (this only works if you operate a
 #               local instance of MediaWiki, see also ../hg/wikiMods/ )
 #    session cookie is used during wiki page edits
 # wiki.sessionCookie=wikidb_mw1__session
 #    URL is the wiki location for the article pages
 #    wikiTrack.URL=http://genomewiki.ucsc.edu
 #    browser to return to from wiki created pages
-# wikiTrack.browser=genome.soe.ucsc.edu
+# wikiTrack.browser=genome.ucsc.edu
 #	You will need to create the namedSessionDb table in your hgcentral db:
 #	hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql
 #  See notes about this in the source tree: src/hg/wikiMods/
 
 #  List of wiki user names that have super user edit privileges
 #	to wiki track items.  Currently this is only a delete item privilege.
 # wikiTrack.editors=Hiram
 #    List of databases to enable the wikiTrack function
 # wikiTrack.dbList=hg18,mm9,hg19
 
 #  New browser function as of April 2007, custom track data is kept
 #	in a database instead of in trash files.  This function requires
 #	several other factors to be in place before it will work.
 #  This was an optional feature for quite some time in 2007 and 2008,
 #	but it is now mandatory.  The older file-based trash system will