05a7268d74bfe3d74f633b1bc1123d6bf1d418c0
jcasper
  Sun Jan 15 01:11:32 2017 -0800
Installing updated hg.conf files from UCSC servers

diff --git confs/preview.hg.conf confs/preview.hg.conf
index e69de29..d0fef62 100644
--- confs/preview.hg.conf
+++ confs/preview.hg.conf
@@ -0,0 +1,244 @@
+###########################################################
+# 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).
+# Change to survey=off (or remove survey setting) to retire the 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.
+
+# survey=https://www.surveymonkey.com/s/5YYTRWQ
+# surveyLabel=2011 ENCODE Usability Survey 
+
+# survey=on
+
+# 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
+#	version as default:
+#	hgsql -e 'update defaultDb set name="mm8" where genome="Mouse"
+#	then this defaultGenome would read: defaultGenome=Mouse
+# 
+defaultGenome=Human
+
+# trackDb table to use. A simple value of `trackDb' is normally sufficient.
+# In general, the value is a comma-separated list of trackDb format tables to
+# search.  This supports local tracks combined with a mirror of the trackDb
+# table from UCSC. The names should be in the form `trackDb_suffix'. This
+# implies a parallel hgFindSpec format search table exists in the form
+# hgFindSpec_suffix.  The specified trackDb tables are searched in the order
+# specified, with the first occurance of a track being used.  You may associate
+# trackDb/hgFindSpec tables with other instances of genome databases using a
+# specification of profile:trackDbTbl, where profile is the name of a
+# databases profile in hg.conf, and trackDbTbl is the name of the table in the
+# remote databases.
+# 
+db.trackDb=trackDb
+#db.trackDb=trackDb_local,trackDb
+#db.trackDb=trackDb,remoteDbs:trackDb
+
+# track group table definitions.  This is a comma-seperate list similar to
+# db.trackDb that defines the track group tables.  Database profiles 
+# may alow be included using the syntax profile:grpTbl.
+db.grp=grp
+#db.grp=grp_local,grp
+#db.grp=grp,remoteDbs:grp
+
+#  New browser function as of March 2007, allowing saved genome browser
+#	sessions into genomewiki
+# wiki.host=genomewiki.ucsc.edu
+# Specify which login system to use, hgLogin CGI or if commented out, the wiki.
+login.systemName=hgLogin CGI
+wiki.host=hgwdev.soe.ucsc.edu
+wiki.userNameCookie=wikidb_mw1_UserName
+wiki.loggedInCookie=wikidb_mw1_UserID
+#wiki.sessionCookie=wikidb_mw1__session
+
+# Settings to allow mirrors to set their own mail signature and return email address for hgLogin
+# emails.
+login.browserName=UCSC Genome Browser
+login.browserAddr=http://genome.ucsc.edu
+login.mailSignature=UCSC Genome Browser Staff
+login.mailReturnAddr=genome-www@soe.ucsc.edu
+
+# wikiTrack function turned on 2009
+#  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.cse.ucsc.edu
+
+#  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
+
+#	tmpdir of /data/tmp is the default location if not specified here
+#	Set this to a directory as recommended in the genomewiki
+#	discussion mentioned above.
+
+# New browser function as of March 2007.  Future browser code will
+#	have this on by default, and can be turned off with =off
+#   Initial release of this function requires it to be turned on here.
+browser.indelOptions=on
+#
+# There are additional fonts available, not all are perfect.
+# Uncomment this to see extra font selections in the configure page
+# fonts.extra=yes
+
+# central.host is the name of the host of the central MySQL
+# database where stuff common to all versions of the genome
+# and the user database is stored.
+central.db=hgcentraltest
+central.host=localhost
+
+# use this cookie setting to keep your installation hguid cookie setting
+#	distinct from UCSC hguid cookie
+central.cookie=hguid.genome-preview
+#	personalize the background of the browser with a specified jpg
+#	floret.jpg is the standard UCSC default
+browser.background=../images/floretPreview.jpg
+
+# Change this default documentRoot if different in your installation,
+#	to allow some of the browser cgi binaries to find help text files
+browser.documentRoot=/usr/local/apache/htdocs
+#	personalize the background of CGIs that don't use images
+#browser.bgcolor=FFF9D2
+
+# optional location of grepIndex files
+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
+
+# 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
+# value has different meaning than an empty value:
+#   delete archivecentral.db [othervars ...]
+
+# Option to disable the "All Tables" query in the table browser.  Useful if
+# one wants to be restrictive about what tables can be seen.
+#   hgta.disableAllTables=yes
+
+# If this option is enabled, the browser CGIs will attempt to generate a an
+# stack traceback on error and dump it to stderr (which is normally captured
+# in the web server error log).  This requires the pstack package to be
+# install, which is available on for unix and linux systems.  If
+# signalsHandler is enabled, the stack will also be printed when a signal
+# indicating an error occurs.
+browser.dumpStack=on
+# log signals
+signalsHandler=on
+
+# These settings enable geographic allele frequency images on the 
+# details pages for the HGDP Allele Frequency (hgdpGeo) track.
+# (HGDP = Human Genome Diversity Project)
+# Programs required for per-SNP geographic maps of HGDP population
+# allele frequencies:
+hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy
+hgc.ps2rasterPath=/hive/data/outside/GMT4.3.1/bin/ps2raster
+hgc.ghostscriptPath=/usr/bin/ghostscript
+
+# Customize your downloads.server machine name here
+downloads.server=hgdownload-test.cse.ucsc.edu
+
+# enable user specific javascript
+# browser.javaScriptDir=js/<your logname>
+
+# enable http(s) proxy support in net.c
+#httpProxy=http://someProxyServer:443/
+# if proxy server needs BASIC authentication
+#httpProxy=http://user:password@someProxyServer:443/
+
+##
+# Database profiles
+##
+#   The dbProfile facility provides a limited mechanism for access tracks from
+# multiple database servers.  This is particularly useful when a mirror server
+# contains the majority of the track data needs to be shared by multiple
+# groups with a small number of locally produced tracks that they the need to
+# keep isolated from the other groups.  A dbProfile associates a MySQL host,
+# user, and password with a dbProfile name.  To define a dbProfile named
+# myProfile, define the hg.conf variables:
+#
+#    myProfile.host
+#    myProfile.user
+#    myProfile.host
+#
+# The default profile is named `db', and is defined by the `db.*' variables
+# described above.  The `customTracks.*' and `central.*' variables also define
+# profiles.
+#
+# Profiles can be associated with an entire genome databases or some types of
+# tables.  To associated with a database, myGenome with myProfile, define the
+# variable:
+#     myGenome.profile=myProfile
+#
+# A dbProfile may be associated with a trackDb/hgFindSpec table pair or a grp
+# table as described in the `db.trackDb' and `db.grp' variables above.  To
+# associate a particular track table, specify the "dbProfile" setting in the
+# trackDb entry:
+#
+#    track myTrack
+#    ...
+#    dbProfile myProfile
+#
+# Note that dbProfile only works on a small number of track types and is not
+# well tested.  In general, the dbProfile facility has not been widely use and
+# may still contain bugs.  The recommended approach for setting up a
+# remote/local server pair is to use the default profile for the remote server
+# with the majority of tracks, and use a non-default profile for local tracks
+# and trackDb tables.  A common configuration would be:
+
+#db.host=oursharedhost
+#db.user=readonly
+#db.password=access
+#
+#myStuff.host=localhost
+#myStuff.user=readonly
+#myStuff.password=access
+#
+#db.trackDb=myStuff:trackDb,trackDb
+#db.grp=myStuffgrp,grp
+
+# Log visible tracks to error_log
+trackLog=on
+
+# Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
+hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js
+
+# let people look at feature-based tracks as coverage wiggles
+canDoCoverage=on