src/product/ex.hg.conf 1.18
1.18 2009/11/18 01:10:54 hiram
Brought up to date on the occassion of losing the copy on genome-test
Index: src/product/ex.hg.conf
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/product/ex.hg.conf,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 1000000 -r1.17 -r1.18
--- src/product/ex.hg.conf 27 Aug 2009 23:09:51 -0000 1.17
+++ src/product/ex.hg.conf 18 Nov 2009 01:10:54 -0000 1.18
@@ -1,141 +1,181 @@
###########################################################
# 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
-
-# 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
-
# 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
# 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>
+
+# Customize your downloads.server machine name here
+# downloads.server=<your download server machine>
+
+# enable user specific javascript
+# browser.javaScriptDir=js/<your logname>