a418bdda66692d67fe8406c90bc06d78fff553e2 jcasper Sun Jul 22 01:11:40 2018 -0700 Installing updated hg.conf files from UCSC servers diff --git confs/hgwbeta.hg.conf confs/hgwbeta.hg.conf index 6b9b4ec..e69de29 100644 --- confs/hgwbeta.hg.conf +++ confs/hgwbeta.hg.conf @@ -1,187 +0,0 @@ - -# 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