320ffaf706be3ac10810765b5f686f6049dbaa66 jcasper Sun Aug 19 01:12:20 2018 -0700 Installing updated hg.conf files from UCSC servers diff --git confs/preview.hg.conf confs/preview.hg.conf index d0fef62..e69de29 100644 --- confs/preview.hg.conf +++ confs/preview.hg.conf @@ -1,244 +0,0 @@ -########################################################### -# 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 - -# 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 - -# 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 - -# Log visible tracks to error_log -trackLog=on - -# Display phylogenetic tree in hgGateway (URL relative to cgi-bin) -hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js - -# let people look at feature-based tracks as coverage wiggles -canDoCoverage=on