e3ebdd69c0eb45cccd5d8564db3f5770b897d22c jcasper Sun Apr 24 01:11:51 2022 -0700 Installing updated hg.conf files from UCSC servers diff --git confs/rr.hg.conf confs/rr.hg.conf index 0dad985..9dee926 100644 --- confs/rr.hg.conf +++ confs/rr.hg.conf @@ -1,196 +1,200 @@ # # 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 # Commented out by request from dschmelt 10/05/18 login.systemName=hgLogin CGI #wiki.host=genome.ucsc.edu 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 # Comment out to turn off survey link in hgTracks # survey=on udc.cacheDir=../trash/udcCache # log stack dumps browser.dumpStack=on # because Galt told us to do it 04/04/11 signalsHandler=on # Transient setting that activates link on hgTracks and # hgGateway for ENCODE/modENCODE survey (March 2010). # Change to survey=off (or remove survey setting) to retire the survey. #survey=on #survey=https://www.surveymonkey.com/s/5YYTRWQ #surveyLabel=2011 ENCODE Usability Survey # 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=1 #survey=on #survey=https://www.surveymonkey.com/r/QYVSXKW # Log visible tracks to error_log trackLog=on # location of CRAM reference sequences cramRef=/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 # 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/rr 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 # Enable hgPhyloPlace: hgPhyloPlaceEnabled=on nextstrainHost=https://nextstrain.org # Recommended track sets refs #25601 browser.recTrackSets=on # Enable FreeType fonts freeType=on freeTypeDir=../htdocs/urw-fonts # Enable mouseover display for wiggles: -mouseOverEnabled=on +# commented by request from Lou 4/20/22 - scheduled for termination +# mouseOverEnabled=on # Move multi-region button above image -multiRegionButtonTop=on +# commented by request from Lou 4/20/22 - scheduled for termination +# multiRegionButtonTop=on # prefix to genark hubs genarkHubPrefix=https://hgdownload.soe.ucsc.edu/hubs # Turns on cart edits and versioning, 7/1/21 -cartVersion=on +# commented by request from Lou 4/20/22 - scheduled for termination +# cartVersion=on # 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 # Enable svg based bar charts -svgBarChart=on +# commented by request from Lou 4/20/22 - scheduled for termination +# svgBarChart=on # 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