5ee234fd2e186bd069a5192118f73a1bc4e80dbd
jcasper
  Sun Sep 26 01:11:54 2021 -0700
Installing updated hg.conf files from UCSC servers

diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf
index f1dfde1..beeb20a 100644
--- confs/hgwdev.hg.conf
+++ confs/hgwdev.hg.conf
@@ -1,392 +1,392 @@
 #hgMirror does not make sense and does not work on hgwdev. You cannot copy over
 #tracks from hgdownload to hgMirror as just a normal apache user.
 #However, it can be useful for ML questions to find out how much disk space a
 #track requires 
 #allowHgMirror=1
 #
 #########################################################
 # 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
 
 allowHgMirror=1
 
 # temporary setting for QA, pending a better way to package dot 
 # with the browser (static binary?)
 graphvizPath=/usr/local/apache/cgi-bin/loader/dot_static
 
 # Transient setting that activates link on hgTracks and 
 # hgGateway for ENCODE/modENCODE survey (March 2010).
 # Remove survey setting to retire the survey.
-survey=http://www.surveymonkey.com/s/XV666V5
-surveyLabel=Test Survey
+#survey=http://www.surveymonkey.com/s/XV666V5
+#surveyLabel=Test Survey
 # survey=http://www.surveymonkey.com//s/XJF93F5
 # surveyLabel=Apply for free workshop
 # survey=http://genome-test.soe.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.
 #    survey=https://www.bit.ly/ucscTraining
 #    surveyLabel=More on-site workshops available!
 # survey=/index.html#newGateway
 # surveyLabel=New User Interface Coming May 10, 2016!
 #survey=https://www.surveymonkey.com/r/QYVSXKW
 #surveyLabel=Take our feedback survey!
 #surveyLabelImage=../images/surveyButton.jpg
 #survey=http://bit.ly/ucscTraining
 #surveyLabel= Request onsite workshops
 #surveyLabel=See us FREE @ ASHG Wed 7:15 am
 #survey=http://bit.ly/ucscAshg2018
 
 # 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
 
 # tracks display width has a default maximum width of 5000 pixels
 # override that limit with a larger number for maxDisplayPixelWidth
 maxDisplayPixelWidth=25600
 
 # 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 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
 #  as below. Note, do not set the values of the two cookies to other
 #  value.
 
 login.systemName=hgLogin CGI
 login.browserName=genome-test Genome Browser
 login.browserAddr=http://genome-test.soe.ucsc.edu
 login.mailSignature=UCSC Genome Browser Administrator
 login.mailReturnAddr=genome-www@soe.ucsc.edu
 
 #Parameters for suggestion form
 suggest.mailSignature=UCSC Genome Browser Staff
 suggest.mailReturnAddr=genome-www@soe.ucsc.edu
 suggest.browserName=UCSC Genome Browser
 
 # wiki track removed 2018-10-05 - Hiram
 #These wiki-lines are involved in hgLogin
 wiki.userNameCookie=DEVwikidb_mw1_UserName
 wiki.loggedInCookie=DEVwikidb_mw1_UserID
 
 
 # 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
 
 # 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
 
 # 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
 udc.localDir=/gbdb
 
 # 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
 
 # Directory where a static cache of public hub files exists to
 # support hub search.
 #hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawl
 
 # 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.soe.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
 
 # 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
 # if you need to debug your proxy config
 #logProxy=on
 # writes messages to stderr every time proxy is used for ftp, http, or https.
 
 ##
 # 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
 
 # No Sql Injection settings
 # values for level are ignore, logOnly, warn, abort
 noSqlInj.level=abort
 # values for dumpStack are on, off
 noSqlInj.dumpStack=on
 
 # Log visible tracks to error_log
 trackLog=on
 
 # location of CRAM reference sequences
 cramRef=../userdata/cramCache
 #showTableCache=tableList
 
 # Make a custom track with BLAT results
 #useBlatBigPsl=on
 #JKSQL_TRACE=on
 #
 #This following turns on short links for hgSession, allowing the redirect.
 #hgSession.shortLink=on
 
 # Separate directory for files that belong to saved sessions (hgSession).
 # The path must be absolute (starts with /).
 # This directory must be on the same filesystem as trash/ so hard links work.
 # The purpose of this directory is to allow automated cleaning of old files
 # from trash/ while keeping saved session files safe in a different location.
 sessionDataDir=/data/apache/userdata/sessions
 sessionDataDirOld=/data/apache/userdata
 
 # Name prefix of 31 separate databases (one for each day of month, on same
 # server as customTrash, using customTracks.* profile) for custom track
 # database tables that belong to users' saved sessions, analogous to
 # sessionDataDir setting for saved session files.
 # The databases must be named as this prefix followed by {01, 02, 03, ... 31}.
 # For example, if the value is "customData" then the databases are named
 # customData01, customData02, ... customData31.
 sessionDataDbPrefix=customData
 
 # Allow the URL: /cgi-bin/hubApi to produce a WEB page
 # otherwise, it redirects to the help page
 hubApi.allowHtml=on
 
 
 # Allow hgHubConnect to run the hubCheck command
 hgHubConnect.validateHub=on
 
 # Setting speeds up the browser by caching large trackDb (such as big hubs)
 #cacheTrackDbDir=../trash/trackDbCache
 cacheTrackDbDir=/dev/shm/trackDbCache
 
 # Recommended track sets refs #25601
 browser.recTrackSets=on
 #browser.recTrackSetsDetectChange=on
 
 ### Testing mouse over display function 2020-10 - Hiram
 mouseOverEnabled=on
 
 # Enable hgPhyloPlace:
 hgPhyloPlaceEnabled=on
 nextstrainHost=https://nextstrain.org
 
 # Enable svg based bar charts
 svgBarChart=on
 
 # Move multi-region button above image
 multiRegionButtonTop=on
 
 # Related tracks
 db.relatedTrack=relatedTrack
 
 # prefix to genark hubs
 genarkHubPrefix=https://hgdownload.soe.ucsc.edu/hubs
 
 # turn on the cart rewrite system
 cartVersion=on
 
 # Database specific settings
 wuhCor1_TopLink=http://genome.ucsc.edu/goldenPath/help/covidBrowserIntro.html
 wuhCor1_TopLinkLabel=Quick start guide
 
 # temporary for testing, max Aug 27, 2021
 # Uncomment to activate the search link
 searchHelpUrl=../goldenPath/help/query.html
 searchHelpLabel=examples
 
 ### bottleneck delay multiplier for custom tracks, an integer >= 1
 ### useful range here is from 1 to about 10.  This will hogExit
 ### robots that are continuously loading custom tracks.
 customTracks.botCheckMult=5
 ### custom track submitted, additional penalty
 ### botCheckMult  added penalty  decay time
 #	1       140 millis	14 seconds
 #	2       225 millis	22 seconds
 #	3       300 millis	30 seconds
 #	4       375 millis	38 seconds
 #	5       440 millis	45 seconds
 #	6       525 millis	52 seconds
 #	7       600 millis	60 seconds