Index: src/product/ex.hg.conf
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/product/ex.hg.conf,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 1000000 -r1.18 -r1.19
--- src/product/ex.hg.conf	18 Nov 2009 01:10:54 -0000	1.18
+++ src/product/ex.hg.conf	18 Nov 2009 17:36:52 -0000	1.19
@@ -1,181 +1,190 @@
 ###########################################################
 # 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.
 #
 #	This file last updated:
 #	$Id$
 #
 ###########################################################
 # db.host is the name of the MySQL host to connect to
 #  high-volume sites will want a separate database server from the web server
 db.host=localhost
 # db.user is the username is use when connecting to the specified db.host
 #	it needs read-only access.  The browser CGIs do not need
 #	read-write access to the database tables
 db.user=readonly
 # db.password is the password to use with the specified db.user
 db.password=access
 
 # 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
 wiki.userNameCookie=wikidb_mw1_UserName
 wiki.loggedInCookie=wikidb_mw1_UserID
 wiki.sessionCookie=wikidb_mw1__session
 
 # 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
 
 #  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
 #	appear to work, but it does not operate properly, and can not
 #	operate some of the newer types of custom tracks.
 #
 #	See also:
 #	http://genomewiki.ucsc.edu/index.php?title=Using_custom_track_database
 #  Use these settings to provide host, user, and password settings
 customTracks.host=<your specific host name>
 customTracks.user=<your specific MySQL user for this function>
 customTracks.password=<MySQL password for specified user>
 customTracks.useAll=yes
-customTracks.tmpdir=/data/tmp
+customTracks.tmpdir=/data/tmp/ct
 #	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 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=hgcentral
 central.host=localhost
 #
 # Be sure this user has UPDATE AND INSERT privs for hgcentral
 #	The central.domain will allow the browser cookie-cart
 #	function to work.  Set it to your domain.  It can be
 #	central.domain=local
 #	when the same machine is used for MySQL and the Apache
 #	WEB server.  Depends upon how your DNS is configured.
 #
 central.user=readwrite
 central.password=update
 central.domain=.cse.ucsc.edu
 #	personalize the background of the browser with a specified jpg
 #	floret.jpg is the standard UCSC default
 browser.background=../images/floret.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
 #	in case of failure of the above central.host machine,
 #	the following settings will be used to access a secondary
 #	mirror of the database
 backupcentral.db=hgcentral
 backupcentral.host=localhost
 backupcentral.user=readwrite
 backupcentral.password=update
 backupcentral.domain=.cse.ucsc.edu
 #	archivecentral settings are used for archived assemblies
 #	that have been moved to a different machine.
 archivecentral.db=hgcentral
 archivecentral.host=localhost
 archivecentral.user=readwrite
 archivecentral.password=update
 
 # Bottleneck info for taming hyperactive web bots
 bottleneck.host=hgwdev
 bottleneck.port=17776
 
 # directory for temporary bbi file caching
 udc.cacheDir=../trash/udcCache
 
 # 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=<your analytics key>
 
+# 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=<your download server machine>
 
 # enable user specific javascript
 # browser.javaScriptDir=js/<your logname>

