5adcf6bc2904690de7b7b30a83ec8a7a0996abe9 galt Tue Aug 21 00:01:25 2018 -0700 changing cse subdomain to soe diff --git src/browserbox/root/hg.conf.offline src/browserbox/root/hg.conf.offline index 8aef89d..8489518 100644 --- src/browserbox/root/hg.conf.offline +++ src/browserbox/root/hg.conf.offline @@ -1,437 +1,437 @@ # special hg.conf for gbib with deactivated network access to UCSC # redirect /gbdb access to local directory first and fallback to UCSC # add the trailing slash gbdbLoc1=/data/gbdb/ -#gbdbLoc2=http://hgdownload.cse.ucsc.edu/gbdb/ +#gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/ # read mysql data first from localhost and fallback to UCSC db.host=localhost db.user=root db.password=browser db.socket=/var/run/mysqld/mysqld.sock -#slow-db.host=genome-mysql.cse.ucsc.edu +#slow-db.host=genome-mysql.soe.ucsc.edu #slow-db.user=genomep #slow-db.password=password # use a table cache to speed up remote queries showTableCache=tableList # the rnaPlot binary is for the hgGene page rnaPlotPath=/usr/local/bin/RNAplot # galaxy and great cannot work from the box hgta.disableSendOutput=yes # redirect links to Encode PDF files back to UCSC hgEncodeVocabDocBaseUrl=http://genome.ucsc.edu # add a gbib specific html style browser.style=/style/gbib.css # use 2bit files instead of nib forceTwoBit=yes # allow hgMirror to run on this machine allowHgMirror=yes ########################################################### # 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. # # This file last updated: # $Id: ex.hg.conf,v 1.27 2010/06/10 05:16:06 markd Exp $ # # if your MySQL system is configured for a different socket connection, # use the following variables to override the MySQL defaults: # db.socket=/var/lib/mysql/mysql.sock # db.port=3306 # *!# NOTE: the port override will only work when host is *not* localhost # when localhost is used, MySQL may connect via shared memory # connections and not via TCP/IP socket ports # 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 dbProfile:trackDbTbl, where dbProfile is the name of a # databases profile in hg.conf, and trackDbTbl is the name of the table in the # remote databases. See below for details of dbProfile # db.trackDb=trackDb #db.trackDb=trackDb_local,trackDb #db.trackDb=db: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 dbProfile:grpTbl. db.grp=grp #db.grp=grp_local,grp #db.grp=grp,someDbProfile:grp # New browser function as of June 2012: # # The UCSC genome browser is using new hgLogin CGI to replace # sign-in service provided by genomewiki previously. # # To maintain backward compatibility, the hgLogin CGI # reuse most of the genomewiki related configuration parameters such as # host and cookie names. This design make transition from genomewiki # to hgLogin transparent. For current mirror sites with sign-in function # (via a simulated- or locally-installed mediawiki server), as long as # hgLogin is not enabled, all browser functions and current sign-in # functions will work as before. Please refer to # # http://genomewiki.ucsc.edu/index.php/Enabling_hgLogin # # for more details. # # To enable the hgLogin function, set the following 8 parameters as # described below: # login.systemName: must be set to some name to enable hgLogin CGI. # wiki.host: should be set to the host that running the hgLogin CGI. # The host should be in the same domain as value set in # "central.domain". # Set the values of the two cookies to value exactly the same as below. # required to use hgLogin login.systemName=Browser-in-a-Box # url to server hosting hgLogin wiki.host=HTTPHOST # Arbitrary name of cookie holding user name wiki.userNameCookie=gbibUser # Arbitrary name of cookie holding user id wiki.loggedInCookie=gbibUserId # The following 4 parameters are used for UI headings (browserName) and # necessary text string used in emails send out to user. # You should set them to any appropriate local values. # title of host of browser, this text be shown in the user interface of # the login/sign up screens login.browserName=Browser-in-a-Box # base url of browser installed login.browserAddr=http://127.0.0.1:1234 # signature written at the bottom of hgLogin system emails login.mailSignature=None # from/return email address used for system emails login.mailReturnAddr=NOEMAIL # The following 6 parameters are used to set up your browser to accept user suggestions. # After a user submits a suggestion, both the user and the suggestion admin address below # will receive an email containing the suggestion. # email address for the suggestion admin #suggest.mailToAddr=suggestion@myuniversitysoe.edu # sender address for the suggestion email #suggest.mailFromAddr=browserAdministrator@mylab.university.edu # Keyword in the mail subject line to help filter out spam #suggest.filterKeyword=FORYOUREYESONLY ## signature written at the bottom of suggestion emails #suggest.mailSignature=My Lab browser administrator # contact address for suggestion follow up #suggest.mailReturnAddr=browserAdministrator@mylab.university.edu # browser name used in emails #suggest.browserName=myLab Genome Browser # The following instructions for using genomewiki has been replaced by the # new hgLogin function as describe above. The section are preserved here # to serve as a reference for the current mirror site using locally # installed mediawiki for the sign-in function. # New browser function as of March 2007, allowing saved genome browser # sessions into genomewiki. These Cookie names depend upon how # your wiki is configured. The wiki system constructs the cookie # names from its own variables $wgDBname and $wgDBprefix # You can find these in your LocalSettings.php, if $wgDbprefix # is not null the cookie name is: $wgDBname_$wgDBprefix_UserName # if wgDbprefix is null then simply: $wgDBname_UserName # same pattern for _UserID and __session below # The example here is for $wgDBName=wikidb and $wgDBprefix=mw1 # wiki.host=genomewiki.ucsc.edu # wiki.userNameCookie=wikidb_mw1_UserName # wiki.loggedInCookie=wikidb_mw1_UserID # You will need to create the namedSessionDb table in your hgcentral db: # hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql # See notes about this in the source tree: src/hg/wikiMods/ # wikiTrack function turned on 2009 (this only works if you operate a # local instance of MediaWiki, see also ../hg/wikiMods/ ) # session cookie is used during wiki page edits # wiki.sessionCookie=wikidb_mw1__session # 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 +# wikiTrack.browser=genome.soe.ucsc.edu # You will need to create the namedSessionDb table in your hgcentral db: # hgsql hgcentral < yourSourceTree/src/hg/lib/namedSessionDb.sql # See notes about this in the source tree: src/hg/wikiMods/ # 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 # New browser function as of April 2007, custom track data is kept # in a database instead of in trash files. This function requires # several other factors to be in place before it will work. # This was an optional feature for quite some time in 2007 and 2008, # but it is now mandatory. The older file-based trash system will # appear to work, but it does not operate properly, and can not # operate some of the newer types of custom tracks. # # See also: # http://genomewiki.ucsc.edu/index.php?title=Using_custom_track_database # Use these settings to provide host, user, and password settings customTracks.host=localhost customTracks.user=root customTracks.socket=/var/run/mysqld/mysqld.sock customTracks.password=browser customTracks.useAll=yes customTracks.tmpdir=/usr/local/apache/trash/customTrash # 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. # self destruct option June 2011. To avoid problem of lost long running # CGI processes. Default CGI expiration time is 20 minutes, # enable cgiExpireMinutes to change that default. # A time of 0 indicates no expiration time. positive integer only # browser.cgiExpireMinutes=20 # default for cgiTime printout to Apache error_log is "yes" # uncomment this cgiTime=no option to turn off the printouts to error_log # browser.cgiTime=no # 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=hgcentral central.host=localhost # # Be sure this user has UPDATE AND INSERT privs for hgcentral # The central.domain will allow the browser cookie-cart # function to work. Set it to the domain of your Apache # WEB server. For example, if your browser URL is: # http://mylab.university.edu/cgi-bin/hgTracks?db=hg19 # set central.domain to: mylab.university.edu # An exception to this is when multiple virtual hosts share the # same central database and central.cookie setting (see below). # In #that case, domain should be inclusive of all virtual hosts # (e.g. only #.university.edu). # central.user=root central.password=browser central.socket=/var/run/mysqld/mysqld.sock central.domain=HTTPHOST # use this cookie setting to keep your installation hguid cookie setting # distinct from UCSC hguid cookie. If you have *multiple* central # databases for multiple hosts, set a distinct cookie name per # central database. # central.cookie=hguid.mylab # personalize the background of the browser with a specified jpg # floret.jpg is the standard UCSC default browser.background=../images/floret.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 # in case of failure of the above central.host machine, # the following settings will be used to access a secondary # mirror of the database backupcentral.db=hgcentral backupcentral.host=localhost backupcentral.user=root backupcentral.password=browser ## archivecentral settings are used for archived assemblies # that have been moved to a different machine. #archivecentral.db=hgcentral #archivecentral.host=localhost #archivecentral.user=readwrite #archivecentral.password=update # Bottleneck info for taming hyperactive web bots # bottleneck.host=yourHost # bottleneck.port=17776 # directory for temporary bbi file caching, default is /tmp/udcCache # see also: README.udc udc.cacheDir=/data/trash/udcCache # it is OK to specify udc.cachDir=../trash/udcCache # to place it in trash. # 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=12 # how long to wait in seconds for parallel fetch to finish parallelFetch.timeout=90 # 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 #noSqlInj.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=<your analytics key> # 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=/usr/lib/gmt/bin/psxy #hgc.ps2rasterPath=/usr/lib/gmt/bin/ps2raster hgc.ghostscriptPath=/usr/bin/ghostscript # Customize your downloads.server machine name here # This can be used in track html description pages when they use # the variable downloadsServer # Also used by Encode tracks # downloads.server=<your download server machine> # enable user specific javascript # browser.javaScriptDir=js/<your logname> # enable user specific style directory (CSS files) # browser.styleDir=style-public # enable user specific style/images directory # browser.styleImagesDir=style/images-public # enable user specific trix file for track search tool # does substitution on the $db variable # browser.trixFile=/gbdb/$db/trackDb.ix # 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 # ## # Track Data Hub related conf variables ## # email address that appears in the hgHubConnect CGI #hub.emailAddress=browserAdministrator@mylab.university.edu # to use something other than "hubPublic" for the hubPublic table #hub.publicTableName=alternateHubPublicTable # to use something other than "hubStatus" for the hubStatus table #hub.statusTableName=alternateHubStatusTable # time in seconds to wait before re-trying a hub with error status # default is 30 minutes (1800 seconds) #hub.timeToCheck=1800 JKSQL_TRACE=on JKSQL_PROF=on