687d35acc65ff6e5dc22e80c749549ff7d8886ef max Tue Aug 21 13:36:58 2018 -0700 Revert "moving all config files in GBIB to the new .gi.ucsc.edu domain names" Apparently there is no plan to create hgdownload.gi.ucsc.edu. The previous commit was completely useless. This reverts commit e1b3625f3a40bfee5c483284fa7f6b23bf6bd47d. diff --git src/browserbox/root/hg.conf.offline src/browserbox/root/hg.conf.offline index d6ccfcb..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.gi.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.gi.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@myuniversity.edu +#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.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= # 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= # enable user specific javascript # browser.javaScriptDir=js/ # 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