a31f1cb3985e86081340007166c0fc64b0f6d4b4
braney
  Wed Dec 12 11:59:24 2012 -0800
add hgwdev hg.conf to kent tree. #8383
diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf
new file mode 100644
index 0000000..8eece49
--- /dev/null
+++ confs/hgwdev.hg.conf
@@ -0,0 +1,269 @@
+#########################################################
+# 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.users
+
+# 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.
+
+
+# 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
+#	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
+
+#  New browser function as of May 2012, using stand alone hgLogin CGI
+#  login system to replace authentication service provided by
+#  genomewiki.
+#  To enable the hgLogin function, set the login.systemName and
+#  wiki.host
+#  as below. Note, do not set the values of the two cookies to other
+#  value.
+
+login.systemName=hgLogin CGI
+login.browserName=hgwdev Genome Browser
+login.browserAddr=http://genome.ucsc.edu
+login.mailSignature=UCSC Genome Browser Administrator
+login.mailReturnAddr=genome-www@soe.ucsc.edu
+
+#wiki.host=genome.ucsc.edu
+wiki.host=hgwdev.cse.ucsc.edu
+#wiki.host=genomewiki.cse.ucsc.edu
+wiki.userNameCookie=wikidb_mw1_UserName
+wiki.loggedInCookie=wikidb_mw1_UserID
+wiki.sessionCookie=wikidb_mw1__session
+
+# wikiTrack function turned on 2009, set read-only June 2012
+wikiTrack.readOnly=yes
+#  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
+
+# self destruct option June 2011.  To avoid problem of lost long running
+#	CGI processes.  Default CGI expiration time is 20 minutes,
+#	enable cgiExpireMinutes to change that default.
+#	A time of 0 indicates no expiration time.  positive integer only
+browser.cgiExpireMinutes=5
+
+# 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
+
+# Turn this back on after people look at genome-test
+# browser.style=../style/genome-test.css
+
+#       add config option to let users personalize background and style
+#       of the browser. Setting is saved in the cart and can be set from
+#       the configure page.
+#       format is browser.theme.<name>=<stylesheet>[,<background>]
+#       background file is optional
+# browser.theme.classic=,../images/floretTest.jpg
+# browser.theme.sansSerif=theme-modern.css,http://silverlight.net/content/samples/sl2/silverlightairlines/run/Images/Background.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
+
+# 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
+
+# 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
+# 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
+
+#  turn on google analytics by setting this key.  This is the identifier
+#	specified by your analytics account
+#  set key for analytics account, used in the getTracker(key) function
+#analyticsKey=UA-4289047-3
+
+# 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
+
+# Temporary flag to help disable new custom track validator if needed
+# If you turn the flag off, it reverts to the old validator 
+newCustomTrackValidate=on
+
+
+# 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.password
+#
+# 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
+#
+# set browser.javaScriptDir for per-developer javascript in trees that do NOT have their own DocumentRoot
+# browser.javaScriptDir=js/<your userid here>
+
+#tell hdb.c code that this is our development server
+test.dev=on