4f4b346461ccd03fb2874ac91e78dd13335689c6 jcasper Sun Mar 3 01:11:26 2024 -0800 Installing updated hg.conf files from UCSC servers diff --git confs/asia.hg.conf confs/asia.hg.conf index ec5cea1..1016b8b 100644 --- confs/asia.hg.conf +++ confs/asia.hg.conf @@ -1,206 +1,213 @@ # 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 #Allow hgHubConnect to run the hubCheck command hgHubConnect.validateHub=on # 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 the hgTracks download track data in window interface popup showDownloadUi=on # allows merging of carts - needed so that recommended track sets do not overwrite your own custom data #28525. Note to delete in future as we want this default mergeRecommended=on # show a message when hgTracks takes longer than X seconds to load warnSeconds=40 # Enables the snake display option canSnake=on # new GA4 key analyticsKey=G-LGP1NRZN4H # show a tutorial on hgTracks to new users showTutorial=on + +# 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