0f235a902415287fde42129404f2f9583789bada
jcasper
Sun Oct 20 01:11:22 2024 -0700
Installing updated hg.conf files from UCSC servers
diff --git confs/asia.hg.conf confs/asia.hg.conf
index 04bf84b..96f85fb 100644
--- confs/asia.hg.conf
+++ confs/asia.hg.conf
@@ -1,223 +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=90
# 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
# 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=What is human CHM13-T2T?
# 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
-
-#Temporary banner to promote the clinical tutorial
-hg38_TopLink=/goldenPath/newsarch.html#100124
-hg38_TopLinkLabel=Try our new clinical tutorial!
-hg19_TopLink=/goldenPath/newsarch.html#100124
-hg19_TopLinkLabel=Try our new clinical tutorial!