a31f1cb3985e86081340007166c0fc64b0f6d4b4 braney Wed Dec 12 11:59:24 2012 -0800 add hgwdev hg.conf to kent tree. #8383 diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf new file mode 100644 index 0000000..8eece49 --- /dev/null +++ confs/hgwdev.hg.conf @@ -0,0 +1,269 @@ +######################################################### +# 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.users + +# Transient setting that activates link on hgTracks and +# hgGateway for ENCODE/modENCODE survey (March 2010). +#survey=on +# Change to survey=off (or remove survey setting) to retire the survey. +# survey=https://www.surveymonkey.com/s/5YYTRWQ +# surveyLabel=2011 ENCODE Usability 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=<BR>Trouble viewing the browser? Reload this web page. +# 2012-03-16: +# survey=https://www.surveymonkey.com/s/ucsc2012 +# surveyLabel=Survey. Help us improve the Browser. + + +# 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 + +# 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 + +# New browser function as of May 2012, using stand alone hgLogin CGI +# login system to replace authentication service provided by +# genomewiki. +# To enable the hgLogin function, set the login.systemName and +# wiki.host +# as below. Note, do not set the values of the two cookies to other +# value. + +login.systemName=hgLogin CGI +login.browserName=hgwdev Genome Browser +login.browserAddr=http://genome.ucsc.edu +login.mailSignature=UCSC Genome Browser Administrator +login.mailReturnAddr=genome-www@soe.ucsc.edu + +#wiki.host=genome.ucsc.edu +wiki.host=hgwdev.cse.ucsc.edu +#wiki.host=genomewiki.cse.ucsc.edu +wiki.userNameCookie=wikidb_mw1_UserName +wiki.loggedInCookie=wikidb_mw1_UserID +wiki.sessionCookie=wikidb_mw1__session + +# wikiTrack function turned on 2009, set read-only June 2012 +wikiTrack.readOnly=yes +# 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 + +# 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=5 + +# 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 + +# Turn this back on after people look at genome-test +# browser.style=../style/genome-test.css + +# add config option to let users personalize background and style +# of the browser. Setting is saved in the cart and can be set from +# the configure page. +# format is browser.theme.<name>=<stylesheet>[,<background>] +# background file is optional +# browser.theme.classic=,../images/floretTest.jpg +# browser.theme.sansSerif=theme-modern.css,http://silverlight.net/content/samples/sl2/silverlightairlines/run/Images/Background.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 + +# optional location of grepIndex files +# braney commented out the following like on 8/29/2012 for testing purposes +#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 + +# 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=100 +# 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 + +# 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 + +# Temporary flag to help disable new custom track validator if needed +# If you turn the flag off, it reverts to the old validator +newCustomTrackValidate=on + + +# 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.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 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 +# +# set browser.javaScriptDir for per-developer javascript in trees that do NOT have their own DocumentRoot +# browser.javaScriptDir=js/<your userid here> + +#tell hdb.c code that this is our development server +test.dev=on