1b4e4c4e1ae303ef3ed233746fd153a30c9f896a jcasper Sun Jan 28 01:11:34 2018 -0800 Installing updated hg.conf files from UCSC servers diff --git confs/hgwdev.hg.conf confs/hgwdev.hg.conf index 3715bff..caee0a6 100644 --- confs/hgwdev.hg.conf +++ confs/hgwdev.hg.conf @@ -1,328 +1,331 @@ #hgMirror does not make sense and does not work on hgwdev. You cannot copy over #tracks from hgdownload to hgMirror as just a normal apache user. #However, it can be useful for ML questions to find out how much disk space a #track requires #allowHgMirror=1 # ######################################################### # 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 allowHgMirror=1 # temporary setting for QA, pending a better way to package dot # with the browser (static binary?) graphvizPath=/usr/local/apache/cgi-bin/loader/dot_static # Transient setting that activates link on hgTracks and # hgGateway for ENCODE/modENCODE survey (March 2010). # 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. # 2012-03-16: # survey=https://www.surveymonkey.com/s/ucsc2012 # surveyLabel=Survey. Help us improve the Browser. # survey=https://www.bit.ly/ucscTraining # surveyLabel=More on-site workshops available! # survey=/index.html#newGateway # surveyLabel=New User Interface Coming May 10, 2016! #survey=https://www.surveymonkey.com/r/QYVSXKW #surveyLabel=Take our feedback survey! #surveyLabelImage=../images/surveyButton.jpg +survey=http://bit.ly/ucscTraining +surveyLabel= Request onsite workshops + # 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 # tracks display width has a default maximum width of 5000 pixels # override that limit with a larger number for maxDisplayPixelWidth maxDisplayPixelWidth=25600 # 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 # 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 login.browserName=genome-test Genome Browser login.browserAddr=http://genome-test.soe.ucsc.edu login.mailSignature=UCSC Genome Browser Administrator login.mailReturnAddr=genome-www@soe.ucsc.edu #Parameters for suggestion form suggest.mailSignature=UCSC Genome Browser Staff suggest.mailReturnAddr=genome-www@soe.ucsc.edu suggest.browserName=UCSC Genome Browser #wiki.host=genome.ucsc.edu wiki.host=HTTPHOST #wiki.host=genomewiki.cse.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID wiki.sessionCookie=wikidb_mw1__session # 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 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 # 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=5 # 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 # Turn this back on after people look at genome-test # browser.style=../style/genome-test.css # add config option to let users personalize background and style # of the browser. Setting is saved in the cart and can be set from # the configure page. # format is browser.theme.<name>=<stylesheet>[,<background>] # background file is optional # browser.theme.classic=,../images/floretTest.jpg # browser.theme.sansSerif=theme-modern.css,http://silverlight.net/content/samples/sl2/silverlightairlines/run/Images/Background.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 # optional location of grepIndex files # braney commented out the following like on 8/29/2012 for testing purposes grepIndex.genbank=/data/tmp/grepIndex grepIndex.default=/gbdb # new option for track reording functions, August 2006 hgTracks.trackReordering=on # 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 udc.localDir=/gbdb/hubs # 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 # Directory where a static cache of public hub files exists to # support hub search. hgHubConnect.cacheDir=../trash/hgHubConnect/hubCrawl # 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 # 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 # 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 # 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 # if you need to debug your proxy config #logProxy=on # writes messages to stderr every time proxy is used for ftp, http, or https. ## # 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 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 # # set browser.javaScriptDir for per-developer javascript in trees that do NOT have their own DocumentRoot # browser.javaScriptDir=js/<your userid here> # #tell hdb.c code that this is our development server test.dev=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 # Log visible tracks to error_log trackLog=on # location of CRAM reference sequences cramRef=../userdata/cramCache #showTableCache=tableList # Display phylogenetic tree in hgGateway (URL relative to cgi-bin) hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js # Make a custom track with BLAT results #useBlatBigPsl=on #JKSQL_TRACE=on