63c70e73aa73f2ccac190a85b1e43edd988d31ac
jcasper
  Wed Mar 2 15:33:44 2016 -0800
Installing updated hg.conf files from UCSC servers

diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf
index de6bacc..2b601ad 100644
--- confs/hgwdev.hg.conf
+++ confs/hgwdev.hg.conf
@@ -1,44 +1,51 @@
+#hgMirror does not make sense and does not work on hgwdev. You cannot copy over
+#tracks from hgdownload to hgMirror as just a normal apache user.
+#However, it can be useful for ML questions to find out how much disk space a
+#track requires 
+#allowHgMirror=1
+#
 #########################################################
 # Config file for the UCSC Human Genome server
 #
 # the format is in the form of name/value pairs
 # written 'name=value' (note that there is no space between
 # the name and its value.
 #
 #	backup recovery 17 November 2009
 #
 ###########################################################
 
 include hg.conf.private
 
 # Transient setting that activates link on hgTracks and 
 # hgGateway for ENCODE/modENCODE survey (March 2010).
 #survey=on
 # Change to survey=off (or remove survey setting) to retire the survey.
 # survey=https://www.surveymonkey.com/s/5YYTRWQ
 # surveyLabel=2011 ENCODE Usability Survey
 # survey=http://www.surveymonkey.com/s/XV666V5
 # surveyLabel=Take ENCODE Survey
 # survey=http://www.surveymonkey.com//s/XJF93F5
 # surveyLabel=Apply for free workshop
 # survey=http://genome-test.cse.ucsc.edu/goldenPath/help/image.html
 # surveyLabel=<BR>Trouble viewing the browser? Reload this web page.
 # 2012-03-16: 
 # survey=https://www.surveymonkey.com/s/ucsc2012
 # surveyLabel=Survey.  Help us improve the Browser.
-
+#    survey=https://www.bit.ly/ucscTraining
+#    surveyLabel=More on-site workshops available!
 
 # if your MySQL system is configured for a different socket connection,
 # use the following variables to override the MySQL defaults:
 # db.socket=/var/lib/mysql/mysql.sock
 # db.port=3306
 # *!# NOTE: the port override will only work when host is *not* localhost
 #	when localhost is used, MySQL may connect via shared memory
 #	connections and not via TCP/IP socket ports
 
 # if you want a different default species selection on the Gateway
 # page, change this default Human to one of the genomes from the
 #	defaultDb table in hgcentral:
 #	hgsql -e "select genome from defaultDb;" hgcentral
 # If you need a different version of that specific genome, change
 #	the defaultDb table entry, for example, a different mouse genome
@@ -153,30 +160,31 @@
 
 # optional location of grepIndex files
 # braney commented out the following like on 8/29/2012 for testing purposes
 grepIndex.genbank=/data/tmp/grepIndex
 grepIndex.default=/gbdb
 
 #  new option for track reording functions, August 2006
 hgTracks.trackReordering=on
 
 # directory for temporary bbi file caching, default is /tmp/udcCache
 # see also: README.udc
 udc.cacheDir=../trash/udcCache
 
 # Mount point for udcFuse read-only filesystem (must be absolute path!):
 #udcFuse.mountPoint=/data/apache/trash/udcFuse
+udc.localDir=/gbdb/hubs
 
 # Parallel fetching of remote network resources using bigDataUrl such as trackHubs and customTracks
 # how many threads to use (set to 0 to disable)
 parallelFetch.threads=100
 # how long to wait in seconds for parallel fetch to finish
 parallelFetch.timeout=90
 
 # An include directive can be used to read text from other files.  this is
 # especially useful when there are multiple browsers hidden behind virtual
 # hosts.  The path to the include file is either absolute or relative to
 # the including file (*not* relative to the current direct directory).
 #   include ../cgi-bin-default/hg.conf
 
 # A delete directive can be used to delete previouly defined values.
 # this is useful in conjunction with include when an undefined
@@ -275,15 +283,24 @@
 # browser.javaScriptDir=js/<your userid here>
 #
 
 
 #tell hdb.c code that this is our development server
 test.dev=on
 
 # No Sql Injection settings
 # values for level are ignore, logOnly, warn, abort
 noSqlInj.level=abort
 # values for dumpStack are on, off
 noSqlInj.dumpStack=on
 
 # Log visible tracks to error_log
 trackLog=on
+
+# let people look at feature-based tracks as coverage wiggles
+#canDoCoverage=on
+
+# use a central database for genbank metadata
+genbankDb=braNey1
+
+# location of CRAM reference sequences
+cramRef=../trash/cramCache