4ad73d3838c527bded485d8b2881a14ae4935027 galt Tue Aug 27 17:17:07 2013 -0700 do not want bottleneck references in hg.conf, should be in hg.conf.private both for security and consistency diff --git confs/preview.hg.conf confs/preview.hg.conf index 2564175..a2a7b21 100644 --- confs/preview.hg.conf +++ confs/preview.hg.conf @@ -1,245 +1,241 @@ ########################################################### # 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. # # backup recovery 17 November 2009 # ########################################################### include hg.conf.private # 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=http://www.surveymonkey.com/s/XV666V5 # surveyLabel=Take ENCODE Survey # survey=http://www.surveymonkey.com//s/XJF93F5 # surveyLabel=Apply for free workshop # survey=http://genome-test.cse.ucsc.edu/goldenPath/help/image.html # surveyLabel=<BR>Trouble viewing the browser? Reload this web page. # survey=https://www.surveymonkey.com/s/5YYTRWQ # surveyLabel=2011 ENCODE Usability Survey # survey=on # if you want a different default species selection on the Gateway # page, change this default Human to one of the genomes from the # defaultDb table in hgcentral: # hgsql -e "select genome from defaultDb;" hgcentral # If you need a different version of that specific genome, change # the defaultDb table entry, for example, a different mouse genome # version as default: # hgsql -e 'update defaultDb set name="mm8" where genome="Mouse" # then this defaultGenome would read: defaultGenome=Mouse # defaultGenome=Human # trackDb table to use. A simple value of `trackDb' is normally sufficient. # In general, the value is a comma-separated list of trackDb format tables to # search. This supports local tracks combined with a mirror of the trackDb # table from UCSC. The names should be in the form `trackDb_suffix'. This # implies a parallel hgFindSpec format search table exists in the form # hgFindSpec_suffix. The specified trackDb tables are searched in the order # specified, with the first occurance of a track being used. You may associate # trackDb/hgFindSpec tables with other instances of genome databases using a # specification of profile:trackDbTbl, where profile is the name of a # databases profile in hg.conf, and trackDbTbl is the name of the table in the # remote databases. # db.trackDb=trackDb #db.trackDb=trackDb_local,trackDb #db.trackDb=trackDb,remoteDbs:trackDb # track group table definitions. This is a comma-seperate list similar to # db.trackDb that defines the track group tables. Database profiles # may alow be included using the syntax profile:grpTbl. db.grp=grp #db.grp=grp_local,grp #db.grp=grp,remoteDbs:grp # New browser function as of March 2007, allowing saved genome browser # sessions into genomewiki # wiki.host=genomewiki.ucsc.edu # Specify which login system to use, hgLogin CGI or if commented out, the wiki. login.systemName=hgLogin CGI wiki.host=hgwdev.soe.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID #wiki.sessionCookie=wikidb_mw1__session # 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 # URL is the wiki location for the article pages #wikiTrack.URL=http://genomewiki.ucsc.edu # browser to return to from wiki created pages #wikiTrack.browser=genome.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 # tmpdir of /data/tmp is the default location if not specified here # Set this to a directory as recommended in the genomewiki # discussion mentioned above. # New browser function as of March 2007. Future browser code will # have this on by default, and can be turned off with =off # Initial release of this function requires it to be turned on here. browser.indelOptions=on # # There are additional fonts available, not all are perfect. # Uncomment this to see extra font selections in the configure page # fonts.extra=yes # central.host is the name of the host of the central MySQL # database where stuff common to all versions of the genome # and the user database is stored. central.db=hgcentraltest central.host=localhost # use this cookie setting to keep your installation hguid cookie setting # distinct from UCSC hguid cookie central.cookie=hguid.genome-preview # personalize the background of the browser with a specified jpg # floret.jpg is the standard UCSC default browser.background=../images/floretPreview.jpg # Change this default documentRoot if different in your installation, # to allow some of the browser cgi binaries to find help text files browser.documentRoot=/usr/local/apache/htdocs # personalize the background of CGIs that don't use images #browser.bgcolor=FFF9D2 # optional location of grepIndex files grepIndex.genbank=/data/tmp/grepIndex grepIndex.default=/gbdb # new option for track reording functions, August 2006 hgTracks.trackReordering=on -# Bottleneck info for taming hyperactive web bots -bottleneck.host=hgwdev -bottleneck.port=17776 - # directory for temporary bbi file caching, default is /tmp/udcCache # see also: README.udc udc.cacheDir=../trash/udcCache # Mount point for udcFuse read-only filesystem (must be absolute path!): #udcFuse.mountPoint=/data/apache/trash/udcFuse # An include directive can be used to read text from other files. this is # especially useful when there are multiple browsers hidden behind virtual # hosts. The path to the include file is either absolute or relative to # the including file (*not* relative to the current direct directory). # include ../cgi-bin-default/hg.conf # A delete directive can be used to delete previouly defined values. # this is useful in conjunction with include when an undefined # value has different meaning than an empty value: # delete archivecentral.db [othervars ...] # Option to disable the "All Tables" query in the table browser. Useful if # one wants to be restrictive about what tables can be seen. # hgta.disableAllTables=yes # If this option is enabled, the browser CGIs will attempt to generate a an # stack traceback on error and dump it to stderr (which is normally captured # in the web server error log). This requires the pstack package to be # install, which is available on for unix and linux systems. If # signalsHandler is enabled, the stack will also be printed when a signal # indicating an error occurs. browser.dumpStack=on # 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 #analyticsKey=UA-4289047-3 # These settings enable geographic allele frequency images on the # details pages for the HGDP Allele Frequency (hgdpGeo) track. # (HGDP = Human Genome Diversity Project) # 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 # Customize your downloads.server machine name here downloads.server=hgdownload-test.cse.ucsc.edu # enable user specific javascript # browser.javaScriptDir=js/<your logname> # enable http(s) proxy support in net.c #httpProxy=http://someProxyServer:443/ # if proxy server needs BASIC authentication #httpProxy=http://user:password@someProxyServer:443/ ## # Database profiles ## # The dbProfile facility provides a limited mechanism for access tracks from # multiple database servers. This is particularly useful when a mirror server # contains the majority of the track data needs to be shared by multiple # groups with a small number of locally produced tracks that they the need to # keep isolated from the other groups. A dbProfile associates a MySQL host, # user, and password with a dbProfile name. To define a dbProfile named # myProfile, define the hg.conf variables: # # myProfile.host # myProfile.user # myProfile.host # # The default profile is named `db', and is defined by the `db.*' variables # described above. The `customTracks.*' and `central.*' variables also define # profiles. # # Profiles can be associated with an entire genome databases or some types of # tables. To associated with a database, myGenome with myProfile, define the # variable: # myGenome.profile=myProfile # # A dbProfile may be associated with a trackDb/hgFindSpec table pair or a grp # table as described in the `db.trackDb' and `db.grp' variables above. To # associate a particular track table, specify the "dbProfile" setting in the # trackDb entry: # # track myTrack # ... # dbProfile myProfile # # Note that dbProfile only works on a small number of track types and is not # well tested. In general, the dbProfile facility has not been widely use and # may still contain bugs. The recommended approach for setting up a # remote/local server pair is to use the default profile for the remote server # with the majority of tracks, and use a non-default profile for local tracks # and trackDb tables. A common configuration would be: #db.host=oursharedhost #db.user=readonly #db.password=access # #myStuff.host=localhost #myStuff.user=readonly #myStuff.password=access # #db.trackDb=myStuff:trackDb,trackDb #db.grp=myStuffgrp,grp