4ad73d3838c527bded485d8b2881a14ae4935027
galt
Tue Aug 27 17:17:07 2013 -0700
do not want bottleneck references in hg.conf, should be in hg.conf.private both for security and consistency
diff --git confs/preview.hg.conf confs/preview.hg.conf
index 2564175..a2a7b21 100644
--- confs/preview.hg.conf
+++ confs/preview.hg.conf
@@ -1,245 +1,241 @@
###########################################################
# 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=
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
-# Bottleneck info for taming hyperactive web bots
-bottleneck.host=hgwdev
-bottleneck.port=17776
-
# 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
# 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
# enable user specific javascript
# browser.javaScriptDir=js/
# 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