a3b71dd1f4305f4ccec1c532565ec7e0fc0e4127
jcasper
  Sun Mar 9 01:11:17 2025 -0800
Installing updated hg.conf files from UCSC servers

diff --git confs/asia.hg.conf confs/asia.hg.conf
index 846a7f9a2f3..fbd080f7eeb 100644
--- confs/asia.hg.conf
+++ confs/asia.hg.conf
@@ -1,217 +1,217 @@
 # 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. Also, no blank lines should be in
 # this file
 ###########################################################
 
 include hg.conf.private
 
 # trackDb table to use
 db.trackDb=trackDb
 # Comment out to disable new double/query insert highlighting options:
 browser.indelOptions=on
 
 #  /data/tmp is the default tmpdir location, change this if desired elsewhere.
 #  What you want is for it to be on a local filesystem, and it must be
 #  read/write/delete enabled for the Apache browser effective user
 
 # 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
 
 #hgHubConnect
 hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawlPublic
 
 # Setting speeds up the browser by caching large trackDb (such as big hubs)
 cacheTrackDbDir=/dev/shm/trackDbCache
 
 # location of grepIndex files
 grepIndex.genbank=/gbdb/genbank/grepIndex
 grepIndex.default=/gbdb
 
 # wiki items to use the login system in the genomewiki for
 #       session management
 login.systemName=hgLogin CGI
 wiki.host=genome.ucsc.edu
 login.acceptIdx=no
 wiki.userNameCookie=wikidb_mw1_UserName
 wiki.loggedInCookie=wikidb_mw1_UserID
 
 # wiki items used by the wiki track to allow editing and fetching
 #       pages from the genomewiki
 # 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 is the site to create links to for new wiki articles
 #wikiTrack.browser=genome.soe.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.
 #       A comma separated listing of Wiki user names.
 #wikiTrack.editors=Hiram
 #  List of databases to enable the wikiTrack function
 #wikiTrack.dbList=hg18,mm9,hg19
 # session cookie is used during wiki page edits
 #wiki.sessionCookie=wikidb_mw1__session
 
 udc.cacheDir=../trash/udcCache
 
 # log stack dumps
 browser.dumpStack=on
 
 # because Galt told us to do it 04/04/11
 signalsHandler=on
 
 # 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=45
 
 # Login statements requested by Chin on Jul 2, 2012
 login.browserName=UCSC Genome Browser
 login.browserAddr=http://genome.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
 
 # No Sql Injection settings
 # values for level are ignore, logOnly, warn, abort
 noSqlInj.level=abort
 # values for dumpStack are on, off
 noSqlInj.dumpStack=on
 
 #
 browser.node=3
 
 #survey=on
 #survey=https://www.surveymonkey.com/r/QYVSXKW
 
 # Log visible tracks to error_log
 trackLog=on
 
 # location of CRAM reference sequences
 cramRef=/data/userdata/cramCache
 
 # Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
 hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js
 
 # Added as a test requested by Chris Lee
 # useBlatBigPsl=on
 
 # The following turns on short links for hgSession, allowing the redirect.
 # Uncommented on 1/23/19 by request from Brian Lee
 hgSession.shortLink=on
 
 # Allow the URL: /cgi-bin/hubApi to produce a WEB page
 # otherwise, it redirects to the help page, default off
 # hubApi.allowHtml=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=/userdata/sessions/asia
 sessionDataDirOld=/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
 
 # Recommended track sets refs #25601
 browser.recTrackSets=on
 
 # Enable hgPhyloPlace:
 hgPhyloPlaceEnabled=on
 nextstrainHost=https://nextstrain.org
 hgPhyloPlaceServerDir=/userdata/hgPhyloPlace/rr
 
 # Enable FreeType fonts
 freeType=on
 freeTypeDir=../htdocs/urw-fonts
 
 # prefix to genark hubs
-genarkHubPrefix=https://hgdownload.soe.ucsc.edu/hubs
+genarkHubPrefix=/gbdb/genark
 
 # Database specific settings
 wuhCor1_TopLink=http://genome.ucsc.edu/goldenPath/help/covidBrowserIntro.html
 wuhCor1_TopLinkLabel=Quick start guide
 
 # Addition requested by gperez 8/7/21
 # Commented out by request dschmelt 9/20/21
 #analytics.trackButtons=off
 
 ### 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
 
 # Related tracks
 db.relatedTrack=relatedTrack
 
 # HTTPS Certificate Check Settings are: abort warn log none
 httpsCertCheck=log
 
 # domains to whitelist, skip cert checking, space-separated list
 # presence of "noHardwiredExceptions" in the list here
 # turns off the hardwired whitelist exceptions in https.c
 httpsCertCheckDomainExceptions=
 
 # with wildcard for testing:
 #httpsCertCheckDomainExceptions=noHardwiredExceptions *.upf.edu *.igh.cnrs.fr *.med.umich.edu
 
 # Assembly-specific html (e.g. links to more info)
 GCA_009914755.4_html=<b><a target=_blank style='font-size:small; position: absolute; margin-left: 1em' href='/goldenPath/newsarch.html#041222'>What is human CHM13-T2T?</a></b>
 
 # Adding parallel loading on files from /gbdb, refs #29819
 udc.localDir=/gbdb
 
 # Adding curated hubs line by request from Jairo 09/26/22
 curatedHubPrefix=public
 
 # show a message when hgTracks takes longer than X seconds to load
 warnSeconds=40 
 
 # new GA4 key
 analyticsKey=G-Z7QQFEZN0L
 
 # use new mouseovers instead of title tags
 showMouseovers=on
 
 # we trust trackDb to know what tables and files exist on this machine
 # so we won't check at start up
 trustTrackDb=on
 
 # limit memory to 20G
 maxMem=21474836480
 
 # Increases the number of items that can be queried from a bigBed file
 bigBedMaxItems=100000
 
 # Show errors instead of triggering error 500 page
 showEarlyErrors=off
 
 # Enables the pop-up when clicking items option on the configure page
 canDoHgcInPopUp=true
 
 # Enables the grouping feature for track hubs
 trackHubsCanAddGroups=on
 
 # Default itemRgb for bigBed tracks with enough fields (see #28498)
 alwaysItemRgb=on