dc3ed2a6e75dbf6e78411ebd971e292d7eb5c54d jcasper Sun Jul 29 01:11:36 2018 -0700 Installing updated hg.conf files from UCSC servers diff --git confs/hgwbeta.hg.conf confs/hgwbeta.hg.conf index e69de29..6b9b4ec 100644 --- confs/hgwbeta.hg.conf +++ confs/hgwbeta.hg.conf @@ -0,0 +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