af60ebe3356cd181c72985d49b9a682f9a5f24ec chmalee Tue Jun 18 13:17:12 2024 -0700 Add showTutorial hg.conf parameter to ex.hg.conf, refs #33992 diff --git src/product/ex.hg.conf src/product/ex.hg.conf index d0675b0..3f0af84 100644 --- src/product/ex.hg.conf +++ src/product/ex.hg.conf @@ -1,696 +1,704 @@ ########################################################### # 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. # ########################################################### # db.host is the name of the MySQL host to connect to # high-volume sites will want a separate database server from the web server db.host=localhost # db.user is the username is use when connecting to the specified db.host # it needs read-only access. The browser CGIs do not need # read-write access to the database tables db.user=readonly # db.password is the password to use with the specified db.user db.password=access # 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 # slow-db is the name of a MySQL host to fallback to if a query failed # on db.host. This means that tables can be dropped from db.host as long as # they are present on slow-db. #slow-db.host=genome-mysql.soe.ucsc.edu #slow-db.user=genomep #slow-db.password=password # If you have assemblies that exists only on this server but not at UCSC, they have to # be declared here, so that the slow-db code does not try to find them on the # genome-mysql.soe.ucsc.edu server #slow-db.excludeDbs=myGenome,myGenome2 # If the slow-db host is far away (more than a few msecs), a table on db.host # with schema information of the slow-db databases will speed up most tracks. # The table is created with the command "makeTableList" and its name is # specified here. If you activate the command below, AND you also have a genome # assembly database on your local mirror that is not present on # genome-mysql.soe.ucsc.edu, then you will need to run the tool 'makeTableList # <database>' to make your genome usable. The table list is a pretty essential # tool to increase remote data access performance to genomes loaded from UCSC, # via slow-db and gbdbLoc1/2 (see below) and so it is assumed to be present. # The code does not know if a genome is local-only or local-and-UCSC, so the tableList # must be created for local databases if you use the showTableCache speedup. # showTableCache=tableList # If your mysql server is configured to reject the option LOCAL in the command # LOAD DATA INFILE (e.g. in OpenSuse) then you can force the browser to never # use the LOCAL option. Note that for this to work, you have to keep all you # mysql servers on the same machine as the CGIs and these servers must have # file permissions and any security infrastructure like SELinux or AppArmor # setup in a way that allows them to read temporary files that the CGIs # (hgCustom, the custom track loaders) create # db.neverLocal=1 # 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 # tracks display width has a default maximum width of 5000 pixels # override that limit with a larger number for maxDisplayPixelWidth # maxDisplayPixelWidth=5000 # # The maximum number of features that can be read from a bigBed file. # This limits the time spent on loading a bigBed track. In coverage mode, # in theory the user can display millions of features, but loading these # can take too much time. #bigBedMaxItems=10000 # 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 occurrence 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=trackDb,someDbProfile: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". # The special value HTTPHOST for wiki.host will use the # server hostname as supplied by the http request. This allows # login to work if a server is reached under different names. # The default value HTTPHOST should work in all contexts. # Set the values of the two cookies to value exactly the same as below. # required to use hgLogin login.systemName=hgLogin CGI # url to server hosting hgLogin wiki.host=HTTPHOST # Arbitrary name of cookie holding user name wiki.userNameCookie=myLabCookieNameForUserName # Arbitrary name of cookie holding user id wiki.loggedInCookie=myLabCookieNameForUseID # 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=myLab Genome Browser # base url of browser installed login.browserAddr=http://mylab.university.edu # signature written at the bottom of hgLogin system emails login.mailSignature=My Lab browser administrator # from/return email address used for system emails # or NOEMAIL to skip the email confirmation login.mailReturnAddr=browserAdministrator@mylab.university.edu # 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 # if https is on, the user login (hgLogin) redirects the user to https. # To do this, it has to use an absolute link that starts with https and the server # name. In certain circumstances, this is not needed, e.g. when the genome browser # is always using https anyways. If the genome browser runs behind a reverse # proxy, this does not work at all, as the CGI does not know that the connection is # already using HTTPs. In these cases, the following statement will not try to # redirect to HTTPS but just use a normal, relative link during/after the login #login.relativeLink=on # If you do not want to use our hgLogin but want to use HTTP Basic Authentication # (e.g. if you have usernames in an htpasswd file or want to use mod_auth_ldap and # validate users against an LDAP server), then you can activate this here. # login.basicAuth=on # Secret text string (like password) for generating and validating secure login key: login.cookieSalt=longSecretTextString # 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.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=<your specific host name> customTracks.user=<your specific MySQL user for this function> customTracks.password=<MySQL password for specified user> customTracks.useAll=yes customTracks.tmpdir=/data/tmp/ct # 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 # Do not show the generic 500 Apache error, but show the browser error message # instead to the user. showEarlyErrors=on # The opposite: try to suppress very early errors as far as possible as # show a 500 Apache error instead. This somewhat reduces the options for # Cross-Site-Scripting attacks but makes it harder for users to find out # what caused an error, e.g. in custom tracks. # suppressVeryEarlyErrors=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). # The special value HTTPHOST will set the domain to whatever # servername was sent with the last HTTP request. This allows cookies # to work if a server has multiple names. central.user=readwrite central.password=update central.domain=mylab.university.edu # 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 # Configuratuion database containing cart tables. Normally thest in in the # same database as central.db, however can be overriden with these # variables if needed. If any of these are set, all must be set. # cart.db= # cart.host= # cart.user= # cart.password= # 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 # Options to personalize the visual style of the browser # Personalize the background of CGIs that don't use images #browser.bgcolor=FFF9D2 # Add a custom CSS file #browser.style=gbib.css # Give the user a choice between different background images and CSS files #browser.theme.modern=background.png,HGStyle #browser.theme.classic=floret.png,HGStyle-old # 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=readwrite backupcentral.password=update # 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 # Big data files (sequences, bigBed, bigWig, trix, etc) are stored in /gbdb by default. # The directory can be moved to another location on the local file system. # The trailing slash is required. # gbdbLoc1=/usr/local/browser/gbdb/ # If a gbdb file is not available on the local file system, then the browser # can also load it from a webserver. The trailing slash is required. # The browser will first try to load a file via gbdbLoc1 and if the file does # not exist, fall back to gbdbLoc2. # gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/ # 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=/tmp/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) # If not specified at all, the default is used: 20 threads. parallelFetch.threads=20 # 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 # # Option to disable the "Send output to Galaxy/Great" in the table browser # Useful if the server is not reachable from galaxy/great # hgta.disableSendOutput=yes # # Option to change the Galaxy target URL to a different site than the main # Galaxy site at usegalaxy.org. The Galaxy CGI is usually called "tool_runner" # galaxyUrl=http://galaxy-qld.genome.edu.au/tool_runner # # Option to "Send output to GenomeSpace" in the table browser # genomeSpace.dmServer=https://dm.genomespace.org/datamanager # genomeSpace.identityServerUrl=https://identity.genomespace.org/identityServer/basic # # Option to disable .nib directories. If set to "no", the # browser will try to use the .2bit file instead of the .nib files, even if # they are setup in hgcentral.dbDb and <db>.chromInfo. .nib files can then # be deleted from this mirror. # allowNib=no # # Base Url of links to Encode PDF files # When this is set as below, the ENCODE PDF files can be deleted from this # mirror. They will get loaded from UCSC. # hgEncodeVocabDocBaseUrl=http://genome.ucsc.edu # 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 # installed, which is available on for unix and linux systems. If # signalsHandler is enabled, the stack will also be printed when a signal # indicates 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=<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=/hive/data/outside/GMT4.3.1/bin/psxy hgc.ps2rasterPath=/hive/data/outside/GMT4.3.1/bin/ps2raster hgc.ghostscriptPath=/usr/bin/ghostscript # the RNAplot program from the Vienna RNA package # http://www.tbi.univie.ac.at/~ronny/RNA/index.html is used for the RNA # structure plots on the hgGene page. By default it is searched in the # cgi-bin directory itself. # rnaPlotPath=/usr/bin/RNAplot # The 'dot' program from the graphviz package is used by hgGeneGraph # to layout the protein interaction network. We provide a static # binary with the Genome Browser for convenience # graphvizPath=ext/dot_static # # 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 css file # browser.style=/style/mystyle.css # enable user specific trix file for track search tool # does substitution on the $db variable # browser.trixPath=/gbdb/$db/trackDb.ix # HTTPS CERTIFICATE VERIFY # Options are abort, warn, log, or none (currently default is warn) #httpsCertCheck=log # domains to whitelist, skip cert checking, space-separated list #httpsCertCheckDomainExceptions= # PROXY # enable http(s) proxy support in net.c #httpProxy=http://someProxyServer:3128 #httpsProxy=http://someProxyServer:3128 #ftpProxy=ftp://127.0.0.1:2121 # if proxy server needs BASIC authentication #httpProxy=http://user:password@someProxyServer:3128 #httpsProxy=http://user:password@someProxyServer:3128 # if some domain suffixes should not be proxied: #noProxy=ucsc.edu,mit.edu,localhost,127.0.0.1 # enable local file access for custom tracks # By default you have to supply http:// URLs for custom track data, e.g. in bigDataUrls # With this statement, you can allow loading from local files, as long as the path # starts with a specific prefix # udc.localDir=/bamFiles # deactivate local disk caching # The system that loads customTrack and track hubs/assembly hubs (internally called UDC) # caches files on local disk in the trash directory. The main disk format in # OSX does not have the functionality needed ("sparse files"), so you can # switch off this cache. # udc.useLocalDiskCache=off # Directory to find CRAM reference sequences in. If a CRAM reference sequence # is not found in this directory, a request file containing the URL to fetch # the sequence will be created in a subdirectory named "pending". A # subdirectory named "error" will be checked for error messages related to # the fetch of reference sequences. # cramRef=/cramFiles ## # 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.password # # 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 associate 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 # Directory where a static cache of public hub files exists to # support hub search. #hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawl # Log visible tracks to error_log # trackLog=on # warning: this can greatly increase the size of your apache error_log # Display phylogenetic tree in hgGateway (URL relative to cgi-bin) # hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js # Configuration options for creating session thumbnails: # # System path from cgi-bin to an alternate directory to store # thumbnails (default is ../trash/hgPS). #sessionThumbnail.imgDir=../trash/hgPS # Path from cgi-bin to the thumbnail directory as seen from # the web (default is ../trash/hgPS). #sessionThumbnail.webPath=../trash/hgPS # System path to Imagemagick convert executable, in case it's not # in Apache's path. #sessionThumbnail.convertPath=/usr/bin/convert # Suppress creation of thumbnails and associated warnings. Must # be set to "on" to disable thumbnail creation. #sessionThumbnail.suppress=on # deactivate the hgMirror CGI on this machine # hgMirror is currently only supported on the GBIB VirtualMachine # default is 0 # allowHgMirror=1 # use 2bit files instead of nib. This is only relevant in failover mode # e.g. on GBIB/GBIC on-line modes. and for very old assemblies. # Only the assemblies dm1, cb1, hg16, and sacCer1 default to using .nib # files. Default is no. # forceTwoBit=yes # Turn off option to save blat results as a custom track. Default is on. # useBlatBigPsl=off # number of sequences allowed to submit to on-line blat, default is 25 # hgBlat.maxSequenceCount=25 # use a database other than hgFixed for the location of genbank table like gbCdnaInfo # genbankDb=hgFixed # use a table other than clade to hold the mappings from clades to their labels # cladeTableName=clade # # use a table other than genomeClade to hold the mappings from genome to clade # genomeCladeTableName=genomeClade # # use a table other than defaultDb to hold the default assembly for a genome # defaultDbTableName=defaultDb # # use a table other than dbDb to describe attributes of installed assemblies # dbDbTableName=dbDb # # use a table other than userDb to describe the user database # userDbTableName=userDb # put error lines from warnings about bigBeds in the apache error_log # bigWarn=on # # specify the root directory for a CGI to use instead of the directory the script lives in # browser.cgiRoot=/usr/local/apache/cgi-bin # Limit the number of bytes that the custom track loader for MAF or VCF track will read in # customTracks.maxBytes=52428800 # Allows hgHubConnect to run hubCheck and present a tree of errors or the overall hub # layout. Requires the hubCheck program to be present in the loader directory. # On by default but can be turned off with this setting # hgHubConnect.validateHub=off ### mouseOverEnabled turns on display of data values in mouse over of a wiggle ### track. It is on by default. Can be turned off with this off setting: # mouseOverEnabled=off # Move the multi region button in hgTracks from below the browser image to beside the position box # multiRegionButtonTop=on/off # # Turn on the cart rewrite feature # cartVersion=on/off # # Provides support for svgBarCharts in hgc. Needed for certain bar chart hgc images to display # svgBarChart=on/off # show a link on hgTracks at the top-right #survey=http://www.sco.com #surveyLabel=Link to some Unix company # Like the above, but not in yellow and just for a database #wuhCor1_TopLink=http://genome.ucsc.edu/goldenPath/help/covidBrowserIntro.html #wuhCor1_TopLinkLabel=Quick start guide # Similar to a survey link, but you can add a piece of html and configure everything yourself #hgTracksNoteHtml=<span style="color:yellow">Some text</span> # Configure a program to resolve cloud URLs to HTTP URLs. See mirrorManual.txt for details. #resolvProts=fs,drs #resolvCmd=/var/www/tools/urlResolver /var/www/tools/config # user-specific CSS files that can be activated via the configuration menu. # Not active on our main site and still under development # The format is browser.theme.<numberForSorting>.<labelUnderscoresAreSpaces>=<filenameInStyleDirectory> # A filename of "<>" means "no file", just the default CSS settings. #browser.theme.1.Default=<> #browser.theme.2.Classic=theme-classic.css #browser.theme.3.Sans_Serif=theme-modern.css #browser.theme.4.Light_Blue=theme-lightBlue.css #browser.theme.5.Dark=theme-dark.css + +# print the javascript includes to the following external javascript libraries that allow +# the interactive tutorial to work: +# https://cdn.jsdelivr.net/npm/shepherd.js@11.0.1/dist/css/shepherd.css +# https://cdn.jsdelivr.net/npm/shepherd.js@11.0.1/dist/js/shepherd.min.js +# Having this variable off will cause the files to not be included and so the tutorial link +# in the help menu won't work +#showTutorial=on