1b4e4c4e1ae303ef3ed233746fd153a30c9f896a jcasper Sun Jan 28 01:11:34 2018 -0800 Installing updated hg.conf files from UCSC servers diff --git confs/hgwbeta.hg.conf confs/hgwbeta.hg.conf index 1af9a07..23aa6d1 100644 --- confs/hgwbeta.hg.conf +++ confs/hgwbeta.hg.conf @@ -1,184 +1,187 @@ # 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.default=/gbdb # wiki items to use the login system in the genomewiki for # session management # New browser function as of May 2012, using stand alone hgLogin CGI # login system to replace authentication service provided by # genomewiki. # To enable the hgLogin function, set the login.systemName and # wiki.host # as below. Note, do not set the values of the two cookies to other # value. login.systemName=hgLogin CGI wiki.host=hgwbeta.cse.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID # Settings to allow mirrors to set their own mail signature and return email address for hgLogin # emails. login.browserName=UCSC Genome Browser login.browserAddr=http://genome.ucsc.edu login.mailSignature=UCSC Genome Browser Staff login.mailReturnAddr=genome-www@soe.ucsc.edu # 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=hgwbeta.cse.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. 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 #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 # 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 # 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 genomeSpace.dmServer=https://dm.genomespace.org/datamanager genomeSpace.identityServerUrl=https://identity.genomespace.org/identityServer/basic # 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