8636358ffed5c6f6e1018db002309dc119df4216 max Fri Oct 10 17:04:57 2014 -0700 more config file changes for gbib diff --git src/browserbox/root/hg.conf.offline src/browserbox/root/hg.conf.offline new file mode 100644 index 0000000..8aef89d --- /dev/null +++ src/browserbox/root/hg.conf.offline @@ -0,0 +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/ + +# 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.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 +# 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