src/product/ex.hg.conf 1.24
1.24 2010/05/05 16:23:45 hiram
comment out bottleneck setting and add central.cookie information and udcFuse mountPoint
Index: src/product/ex.hg.conf
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/product/ex.hg.conf,v
retrieving revision 1.23
retrieving revision 1.24
diff -b -B -U 1000000 -r1.23 -r1.24
--- src/product/ex.hg.conf 14 Apr 2010 07:56:06 -0000 1.23
+++ src/product/ex.hg.conf 5 May 2010 16:23:45 -0000 1.24
@@ -1,211 +1,217 @@
###########################################################
# 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
# 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
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/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 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=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 the domain of your Apache
# WEB server. For example, if your browser URL is:
# http://mylab.university.edu/cgi-bin/hgTracks?db=hg19
# set central.domain to: mylab.university.edu
#
central.user=readwrite
central.password=update
central.domain=mylab.university.edu
+# use this cookie setting to keep your installation hguid cookie setting
+# distinct from UCSC hguid cookie
+# central.cookie=hguid.mylab
# 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
+# bottleneck.host=yourHost
+# bottleneck.port=17776
# directory for temporary bbi file caching, default is /tmp/udcCache
# see also: README.udc
# udc.cacheDir=/tmp/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
# 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
# This can be used in track html description pages when they use
# the variable downloadsServer
# Also used by Encode tracks
# downloads.server=<your download server machine>
# 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/