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###########################################################
# 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: ex.hg.conf,v 1.27 2010/06/10 05:16:06 markd Exp $
#
###########################################################
# 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 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
# slow-db is the name of a MySQL host to fallback to if a query failed
# on db.host. This means that tables can be dropped from db.host as long as
# they are present on slow-db.
#slow-db.host=genome-mysql.soe.ucsc.edu
#slow-db.user=genomep
#slow-db.password=password
# If the slow-db host is too far away, a table on db.host with schema information
# of the slow-db databases will speed up most tracks. The table is created with
# the command "makeTableList" and its name is specified here
# showTableList=tableList
# If your mysql server is configured to reject the option LOCAL in the command
# LOAD DATA INFILE (e.g. in OpenSuse) then you can force the browser to never
# use the LOCAL option. Note that for this to work, you have to keep all you
# mysql servers on the same machine as the CGIs and these servers must have
# file permissions and any security infrastructure like SELinux or AppArmor
# setup in a way that allows them to read temporary files that the CGIs
# (hgCustom, the custom track loaders) create
# db.neverLocal=1
# 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
# tracks display width has a default maximum width of 5000 pixels
# override that limit with a larger number for maxDisplayPixelWidth
# maxDisplayPixelWidth=5000
# 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 occurrence of a track being used. You may associate
# trackDb/hgFindSpec tables with other instances of genome databases using a
# specification of dbProfile:trackDbTbl, where dbProfile is the name of a
# databases profile in hg.conf, and trackDbTbl is the name of the table in the
# remote databases. See below for details of dbProfile
#
db.trackDb=trackDb
#db.trackDb=trackDb_local,trackDb
#db.trackDb=trackDb,someDbProfile: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 dbProfile:grpTbl.
db.grp=grp
#db.grp=grp_local,grp
#db.grp=grp,someDbProfile:grp
# New browser function as of June 2012:
#
# The UCSC genome browser is using new hgLogin CGI to replace
# sign-in service provided by genomewiki previously.
#
# To maintain backward compatibility, the hgLogin CGI
# reuse most of the genomewiki related configuration parameters such as
# host and cookie names. This design make transition from genomewiki
# to hgLogin transparent. For current mirror sites with sign-in function
# (via a simulated- or locally-installed mediawiki server), as long as
# hgLogin is not enabled, all browser functions and current sign-in
# functions will work as before. Please refer to
#
# http://genomewiki.ucsc.edu/index.php/Enabling_hgLogin
#
# for more details.
#
# To enable the hgLogin function, set the following 8 parameters as
# described below:
# login.systemName: must be set to some name to enable hgLogin CGI.
# wiki.host: should be set to the host that running the hgLogin CGI.
# The host should be in the same domain as value set in
# "central.domain".
# The special value HTTPHOST for wiki.host will use the
# server hostname as supplied by the http request. This allows
# login to work if a server is reached under different names.
# The default value HTTPHOST should work in all contexts.
# Set the values of the two cookies to value exactly the same as below.
# required to use hgLogin
login.systemName=hgLogin CGI
# url to server hosting hgLogin
wiki.host=HTTPHOST
# Arbitrary name of cookie holding user name
wiki.userNameCookie=myLabCookieNameForUserName
# Arbitrary name of cookie holding user id
wiki.loggedInCookie=myLabCookieNameForUseID
# The following 4 parameters are used for UI headings (browserName) and
# necessary text string used in emails send out to user.
# You should set them to any appropriate local values.
# title of host of browser, this text be shown in the user interface of
# the login/sign up screens
login.browserName=myLab Genome Browser
# base url of browser installed
login.browserAddr=http://mylab.university.edu
# signature written at the bottom of hgLogin system emails
login.mailSignature=My Lab browser administrator
# from/return email address used for system emails
# or NOEMAIL to skip the email confirmation
login.mailReturnAddr=browserAdministrator@mylab.university.edu
# If login is enabled, then the server should be configured to support HTTPS.
# HTTPS is used for hgLogin by default. If the server cannot support HTTPS
# but login is still enabled (not recommended), HTTPS for hgLogin can be
# disabled by uncommenting this setting:
#login.https=off
# if https is on, the user login (hgLogin) redirects the user to https.
# To do this, it has to use an absolute link that starts with https and the server
# name. In certain circumstances, this is not needed, e.g. when the genome browser
# is always using https anyways. If the genome browser runs behind a reverse
# proxy, this does not work at all, as the CGI does not know that the connection is
# already using HTTPs. In these cases, the following statement will not try to
# redirect to HTTPS but just use a normal, relative link during/after the login
#login.relativeLink=on
# If you do not want to use our hgLogin but want to use HTTP Basic Authentication
# (e.g. if you have usernames in an htpasswd file or want to use mod_auth_ldap and
# validate users against an LDAP server), then you can activate this here.
# login.basicAuth=on
# Secret text string (like password) for generating and validating secure login key:
login.cookieSalt=longSecretTextString
# The following 6 parameters are used to set up your browser to accept user suggestions.
# After a user submits a suggestion, both the user and the suggestion admin address below
# will receive an email containing the suggestion.
# email address for the suggestion admin
suggest.mailToAddr=suggestion@myuniversitysoe.edu
# sender address for the suggestion email
suggest.mailFromAddr=browserAdministrator@mylab.university.edu
# Keyword in the mail subject line to help filter out spam
suggest.filterKeyword=FORYOUREYESONLY
# signature written at the bottom of suggestion emails
suggest.mailSignature=My Lab browser administrator
# contact address for suggestion follow up
suggest.mailReturnAddr=browserAdministrator@mylab.university.edu
# browser name used in emails
suggest.browserName=myLab Genome Browser
# The following instructions for using genomewiki has been replaced by the
# new hgLogin function as describe above. The section are preserved here
# to serve as a reference for the current mirror site using locally
# installed mediawiki for the sign-in function.
# New browser function as of March 2007, allowing saved genome browser
# sessions into genomewiki. These Cookie names depend upon how
# your wiki is configured. The wiki system constructs the cookie
# names from its own variables $wgDBname and $wgDBprefix
# You can find these in your LocalSettings.php, if $wgDbprefix
# is not null the cookie name is: $wgDBname_$wgDBprefix_UserName
# if wgDbprefix is null then simply: $wgDBname_UserName
# same pattern for _UserID and __session below
# The example here is for $wgDBName=wikidb and $wgDBprefix=mw1
# wiki.host=genomewiki.ucsc.edu
# wiki.userNameCookie=wikidb_mw1_UserName
# wiki.loggedInCookie=wikidb_mw1_UserID
# You will need to create the namedSessionDb table in your hgcentral db:
# hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql
# See notes about this in the source tree: src/hg/wikiMods/
# wikiTrack function turned on 2009 (this only works if you operate a
# local instance of MediaWiki, see also ../hg/wikiMods/ )
# session cookie is used during wiki page edits
# wiki.sessionCookie=wikidb_mw1__session
# 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.soe.ucsc.edu
# You will need to create the namedSessionDb table in your hgcentral db:
# hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql
# See notes about this in the source tree: src/hg/wikiMods/
# 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.
# 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=20
# default for cgiTime printout to Apache error_log is "yes"
# uncomment this cgiTime=no option to turn off the printouts to error_log
# browser.cgiTime=no
# Do not show the generic 500 Apache error, but show the browser error message
# instead to the user.
showEarlyErrors=on
# The opposite: try to suppress very early errors as far as possible as
# show a 500 Apache error instead. This somewhat reduces the options for
# Cross-Site-Scripting attacks but makes it harder for users to find out
# what caused an error, e.g. in custom tracks.
# suppressVeryEarlyErrors=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
# An exception to this is when multiple virtual hosts share the
# same central database and central.cookie setting (see below).
# In #that case, domain should be inclusive of all virtual hosts
# (e.g. only #.university.edu).
# The special value HTTPHOST will set the domain to whatever
# servername was sent with the last HTTP request. This allows cookies
# to work if a server has multiple names.
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. If you have *multiple* central
# databases for multiple hosts, set a distinct cookie name per
# central database.
# 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
# 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
# Big data files (sequences, bigBed, bigWig, trix, etc) are stored in /gbdb by default.
# The directory can be moved to another location on the local file system.
# The trailing slash is required.
# gbdbLoc1=/usr/local/browser/gbdb/
# If a gbdb file is not available on the local file system, then the browser
# can also load it from a webserver. The trailing slash is required.
# The browser will first try to load a file via gbdbLoc1 and if the file does
# not exist, fall back to gbdbLoc2.
# gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/
# Bottleneck info for taming hyperactive web bots
# bottleneck.host=yourHost
# bottleneck.port=17776
# directory for temporary bbi file caching, default is /tmp/udcCache
# see also: README.udc
# udc.cacheDir=/tmp/udcCache
# it is OK to specify udc.cachDir=../trash/udcCache
# to place it in trash.
# 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=20
# 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
#
# Option to disable the "Send output to Galaxy/Great" in the table browser
# Useful if the server is not reachable from galaxy/great
# hgta.disableSendOutput=yes
#
# Option to change the Galaxy target URL to a different site than the main
# Galaxy site at usegalaxy.org. The Galaxy CGI is usually called "tool_runner"
# galaxyUrl=http://galaxy-qld.genome.edu.au/tool_runner
#
# Option to "Send output to GenomeSpace" in the table browser
# genomeSpace.dmServer=https://dm.genomespace.org/datamanager
# genomeSpace.identityServerUrl=https://identity.genomespace.org/identityServer/basic
#
# Option to disable .nib directories. If set to "no", the
# browser will try to use the .2bit file instead of the .nib files, even if
# they are setup in hgcentral.dbDb and <db>.chromInfo. .nib files can then
# be deleted from this mirror.
# allowNib=no
#
# Base Url of links to Encode PDF files
# When this is set as below, the ENCODE PDF files can be deleted from this
# mirror. They will get loaded from UCSC.
# hgEncodeVocabDocBaseUrl=http://genome.ucsc.edu
# 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
# installed, which is available on for unix and linux systems. If
# signalsHandler is enabled, the stack will also be printed when a signal
# indicates 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
# the RNAplot program from the Vienna RNA package
# http://www.tbi.univie.ac.at/~ronny/RNA/index.html is used for the RNA
# structure plots on the hgGene page. By default it is searched in the
# cgi-bin directory itself.
# rnaPlotPath=/usr/bin/RNAplot
# The 'dot' program from the graphviz package is used by hgGeneGraph
# to layout the protein interaction network. We provide a static
# binary with the Genome Browser for convenience
# graphvizPath=ext/dot_static
#
# 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 user specific style directory (CSS files)
# browser.styleDir=style-public
# enable user specific style/images directory
# browser.styleImagesDir=style/images-public
# enable user specific css file
# browser.style=/style/mystyle.css
# enable user specific trix file for track search tool
# does substitution on the $db variable
# browser.trixFile=/gbdb/$db/trackDb.ix
# PROXY
# enable http(s) proxy support in net.c
#httpProxy=http://someProxyServer:3128
#httpsProxy=http://someProxyServer:3128
#ftpProxy=ftp://127.0.0.1:2121
# if proxy server needs BASIC authentication
#httpProxy=http://user:password@someProxyServer:3128
#httpsProxy=http://user:password@someProxyServer:3128
# if some domain suffixes should not be proxied:
#noProxy=ucsc.edu,mit.edu,localhost,127.0.0.1
# enable local file access for custom tracks
# By default you have to supply http:// URLs for custom track data, e.g. in bigDataUrls
# With this statement, you can allow loading from local files, as long as the path
# starts with a specific prefix
# udc.localDir=/bamFiles
# deactivate local disk caching
# The system that loads customTrack and track hubs/assembly hubs (internally called UDC)
# caches files on local disk in the trash directory. The main disk format in
# OSX does not have the functionality needed ("sparse files"), so you can
# switch off this cache.
# udc.useLocalDiskCache=off
# Directory to find CRAM reference sequences in. If a CRAM reference sequence
# is not found in this directory, a request file containing the URL to fetch
# the sequence will be created in a subdirectory named "pending". A
# subdirectory named "error" will be checked for error messages related to
# the fetch of reference sequences.
# cramRef=/cramFiles
##
# 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 associate 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
#
##
# Track Data Hub related conf variables
##
# email address that appears in the hgHubConnect CGI
#hub.emailAddress=browserAdministrator@mylab.university.edu
# to use something other than "hubPublic" for the hubPublic table
#hub.publicTableName=alternateHubPublicTable
# to use something other than "hubStatus" for the hubStatus table
#hub.statusTableName=alternateHubStatusTable
# time in seconds to wait before re-trying a hub with error status
# default is 30 minutes (1800 seconds)
#hub.timeToCheck=1800
# Directory where a static cache of public hub files exists to
# support hub search.
#hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawl
# Log visible tracks to error_log
# trackLog=on
# warning: this can greatly increase the size of your apache error_log
# Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
# hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js
# Configuration options for creating session thumbnails:
#
# System path from cgi-bin to an alternate directory to store
# thumbnails (default is ../trash/hgPS).
#sessionThumbnail.imgDir=../trash/hgPS
# Path from cgi-bin to the thumbnail directory as seen from
# the web (default is ../trash/hgPS).
#sessionThumbnail.webPath=../trash/hgPS
# System path to Imagemagick convert executable, in case it's not
# in Apache's path.
#sessionThumbnail.convertPath=/usr/bin/convert
# Suppress creation of thumbnails and associated warnings. Must
# be set to "on" to disable thumbnail creation.
#sessionThumbnail.suppress=on
# deactivate the hgMirror CGI on this machine
# hgMirror is currently only supported on the GBIB VirtualMachine
# default is 0
# allowHgMirror=1
# use 2bit files instead of nib. This is only relevant in failover mode
# e.g. on GBIB/GBIC on-line modes. and for very old assemblies.
# Only the assemblies dm1, cb1, hg16, and sacCer1 default to using .nib
# files. Default is no.
# forceTwoBit=yes
# Turn off option to save blat results as a custom track. Default is on.
# useBlatBigPsl=off
# number of sequences allowed to submit to on-line blat, default is 25
# hgBlat.maxSequenceCount=25
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