5a6fb43a17ad1a68e6d3d7296537dcc138d6cad0 jcasper Sun Nov 27 01:11:21 2022 -0800 Installing updated hg.conf files from UCSC servers diff --git confs/hgwbeta.hg.conf confs/hgwbeta.hg.conf index fb2419e..25bb355 100644 --- confs/hgwbeta.hg.conf +++ confs/hgwbeta.hg.conf @@ -1,245 +1,246 @@ # 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 # for hgGeneGraph: location of the 'dot' binary # for centos, we use a statically compiled version # as the dot package on centos is too old graphvizPath=/usr/local/apache/cgi-bin/loader/dot_static #versionStamped=on #browser.documentRoot=/usr/local/apache/htdocs-beta #browser.trixPath=/hive/data/inside/trix/$db_trackDb_beta.ix # trackDb table to use db.trackDb=trackDb # changing to relative path (adding "..") browser.background=../images/floretBeta.jpg # Comment out to disable new double/query insert highlighting options: browser.indelOptions=on # track search index name. Since this resides in /gbdb/ then beta must have a uniquely named ix browser.trixPath=/data/trix/$db_trackDb.ix # customTracks database is used to hold custom tracks # For performance and security, it is on a separate server. # The database name is fixed at: customTrash # This is a define CUSTOM_TRASH in hg/inc/customTrack.h # switched to hgwslave on 2009-02-12 about 16:00 #customTracks.host=hgwslave # switched to customdb on 2011-12-06 at 11:00 customTracks.useAll=yes customTracks.tmpdir=/data/tmp/ct # /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 # location of grepIndex files #grepIndex.genbank=/gbdb/genbank/grepIndex grepIndex.genbank=/gbdb/genbank/grepIndex grepIndex.default=/gbdb # Removed wikiTrack info 2018-10-05 #These wiki lines are needed by hgLogin wiki.userNameCookie=BETAwikidb_mw1_UserName wiki.loggedInCookie=BETAwikidb_mw1_UserID # Settings to allow mirrors to set their own mail signature and return email address for hgLogin # emails. login.systemName=hgLogin CGI login.browserName=UCSC Genome Browser login.browserAddr=http://genome.ucsc.edu login.mailSignature=UCSC Genome Browser Staff 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 # Comment out to turn off survey link in hgTracks and hgGateway #cath 7-12-16, Angie says that survey=on is no longer needed. Just uncomment 'survey' and 'surveyLabel' # Change to survey=off (or remove survey setting) to retire the survey. # survey=https://www.surveymonkey.com/s/5YYTRWQ # surveyLabel=2011 ENCODE Usability Survey # survey=https://www.bit.ly/ucscTraining # surveyLabel=More on-site workshops available! #survey=/index.html#newGateway #surveyLabel=New Gateway Coming May 10, 2016! #survey=https://www.surveymonkey.com/r/QYVSXKW #surveyLabel=Take our feedback survey! #surveyLabelImage=../images/surveyButton.jpg # log signals signalsHandler=on # turn on google analytics by setting this key. This is the identifier # specified by your analytics account # set key for analytics account, used in the getTracker(key) function # -3 for hgwdev, -4 for hgw0, -5 for gBiB, -6 for RR analyticsKey=UA-4289047-6 # log stack dumps browser.dumpStack=on # node id # browser.node=2 # 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 udc.cacheDir=../trash/udcCache #makes browser timeout after only 1min (instead of 20min) #browser.cgiExpireMinutes=1 # 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 # 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 # No Sql Injection settings # values for level are ignore, logOnly, warn, abort noSqlInj.level=abort # values for dumpStack are on, off noSqlInj.dumpStack=on # line added to turn off the new hash-enhanced hgsid/uid values #browser.sessionKey=off # HTTPS Certificate Check Settings are: abort warn log none # currently log is the default #httpsCertCheck=none httpsCertCheck=log # domains to whitelist, skip cert checking, space-separated list httpsCertCheckDomainExceptions= # useful for testing, presence of "noHardwiredExceptions" in the list here # turns off the hardwired whitelist exceptions in https.c #httpsCertCheckDomainExceptions=noHardwiredExceptions # with wildcard for testing: #httpsCertCheckDomainExceptions=noHardwiredExceptions *.upf.edu *.igh.cnrs.fr *.med.umich.edu # Apply a maximum to the size of MAF and VCF custom tracks supplied # directly (instead of via bigURLs). #customTracks.maxBytes=52428800 # 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 # Set up thumbnails directory for public sessions CGI sessionThumbnail.imgDir=../trash/hgPS sessionThumbnail.webPath=../trash/hgPS #Turns on short links for hgSession, allowing redirect to full link. hgSession.shortLink=on # If login is enabled, then the server should be configured to support HTTPS. # HTTPS is used for hgLogin by default. If the server cannot support HTTPS # but login is still enabled (not recommended), HTTPS for hgLogin can be # disabled by uncommenting this setting:login.https=off #login.https=off # # Turn off option to save blat results as a custom track. Default is on. #useBlatBigPsl=off # GenomeSpace prod instance urls - turned off 11/18 refs #24044 #genomeSpace.dmServer=https://dm.genomespace.org/datamanager #genomeSpace.identityServerUrl=https://identity.genomespace.org/identityServer/basic # 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/beta 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 # Directory where a static cache of public hub files exists to # support hub search. hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawlBeta #survey=http://bit.ly/ucscTraining #surveyLabel= Request onsite workshops #Outputs every single SQL call in the error logs # JKSQL_TRACE=on # 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=/dev/shm/trackDbCache # Enable hgPhyloPlace: hgPhyloPlaceEnabled=on nextstrainHost=https://nextstrain.org hgPhyloPlaceServerDir=/userdata/hgPhyloPlace/hgwbeta # Recommended track sets refs #25601 browser.recTrackSets=on # Enable FreeType fonts freeType=on #freeTypeDir=/usr/share/fonts/default/Type1 # Database specific settings wuhCor1_TopLink=http://genome.ucsc.edu/goldenPath/help/covidBrowserIntro.html wuhCor1_TopLinkLabel=Quick start guide # Related tracks db.relatedTrack=relatedTrack # prefix to genark hubs genarkHubPrefix=https://hgdownload.soe.ucsc.edu/hubs # Related tracks db.relatedTrack=relatedTrack # 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> curatedHubPrefix=beta udc.localDir=/gbdb +canDupTracks=on