b6cbd59bc90b14b3a643ba42783040e769d238bb
chmalee
  Wed Jul 21 10:44:57 2021 -0700
Add gtexGenev8 to list of tables always downloaded by hgMirror and gbib, since it is a default track on hg38, refs #27854

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index aaea5e8..c3734d4 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -1,523 +1,528 @@
 #!/bin/bash
 
 # update script on the GBiB virtual machine
 # - updates itself and then run itself
 # - updates cgis, html and gbdb via rsync 
 # - patches the menu
 # - calls hgMirror to hide some slow default tracks, e.g. conservation+retro 
 
 # will not run if:
 # - not run as root
 # - if a script named updateBrowser.sh already is running
 # - any hgMirror jobs are running
 # - hgdownload is offline
 # - if a flagFile on hgDownload is not more recent than a local flag file
 # - if the VirtualBox Guest property "gbibAutoUpdateOff" is set. To set it, run this on the host 
 #   "VBoxManage guestproperty set browserbox gbibAutoUpdateOff"
 
 # To find out why the script did not run, use the command echo $? to show the
 # exit code of the script:
 # 1 - not root
 # 2 - already running
 # 3 - no internet connection
 # 4 - hgMirror job is running
 # 5 - not enough arguments
 # 6 - virtualbox guest property is set
 
 # parameters:
 # - parameter "hgwdev": does not update itself, copies only the beta/alpha CGIs/htdocs from hgwdev
 # - parameter "notSelf": does not update itself and does not check flagfile
 
 # this script is not using the bash options pipefail or errabort.
 # In case something goes wrong it continues, this is intentional to 
 # avoid a virtual machine that can not update itself anymore
 
 # rsync options:
 # l = preserve symlinks
 # t = preserve time
 # r = recurse
 # z = compress
 # v = verbose
 # h = human readable
 # u = skip if file is newer on receiver
 # We are not using the -z option anymore because it may cause
 # CPU overload on hgdownload
 RSYNCOPTS="-ltrvh"
 # rsync server for CGIs and html files
 RSYNCSRC="rsync://hgdownload.soe.ucsc.edu"
 RSYNCCGIBIN=cgi-bin
 RSYNCHTDOCS=htdocs
 UPDATEFLAG=http://hgdownload.soe.ucsc.edu/gbib/lastUpdate
 LOGFILE=/var/log/gbibUpdates.log
 DEBUG=0
 if [[ "$#" -ne 0 ]]; then
     DEBUG=1
 fi
 
 # function to echo only if run with some arguments
 function echoDebug {
    if [[ DEBUG -eq "1" ]]; then
      echo $*
    fi
 } 
 
 # make sure that apt-get never opens an interactive dialog
 export DEBIAN_FRONTEND=noninteractive 
 
 # help
 if [ "$1" == "-h" ] ; then
    echo "Without any options, this script checks if it can reach hgdownload and if "
    echo "new data has been added since the last run. It updates itself and runs the new copy."
    echo "The new copy rsyncs the CGIs/MysqlDbs/htdocs from hgdownload."
    echo "It rsyncs the gbib/push directory into / to update other files."
    echo "It finally repairs mysql tables, makes some trackDb changes, adds symlinks,"
    echo "and chmods the directories."
    echo "Parameters:"
    echo "updateBrowser.sh notSelf - do not update the script itself. Do not check if data has been "
    echo "                           added to hgdownload since the last run"
    echo "updateBrowser.sh hgwdev - more info on how to update to alpha versions (used only by UCSC)"
    exit 0
 fi
 
 # check if running as root
 if [ "$(id -u)" != "0" ] ; then
    echo "This script must be run as root" 1>&2
    exit 1
 fi
 
 # check if running already, 3 = the main script + its update + the subshell where this command is running
 RUNNING=`ps --no-headers -CupdateBrowser.sh | wc -l`
 if [ ${RUNNING} -gt 3 ] ; then
     echoDebug GBiB update already running, not starting
     exit 2
 fi
 	
 # if run with no argument (=from cron): check if the VirtualBox guest addition
 # kernel modules work and if yes, if auto-updates were deactivated from the
 # Vbox host via a property
 if [ "$#" -eq 0 ] ; then
     if modprobe vboxguest 2> /dev/null > /dev/null; then
        if VBoxControl guestproperty get gbibAutoUpdateOff | grep -xq "Value: yes" 2> /dev/null ; then
            exit 6
        fi
     fi
 # show a little note when VirtualBox kernel module is not working and we're not running under cron
 else
     if [ ! modprobe vboxguest 2> /dev/null > /dev/null ] ; then
       echo - Info: GBiB not running on VirtualBox or VirtualBox Guest Utils are not working
     fi
 fi
 
 
 # check if we have internet, stop if not
 wget -q --tries=1 --timeout=10 --spider http://hgdownload.soe.ucsc.edu -O /dev/null
 if [ $? -ne 0 ] ; then
     echoDebug GBiB has no connection to hgdownload.soe.ucsc.edu, cannot update now
     exit 3
 fi
 
 # check flag file if run with no parameter (=from cron)
 if [ "$#" -eq 0 ] ; then
    # check a flag file to see if anything on hgdownload actually changed
    if /root/urlIsNotNewerThanFile $UPDATEFLAG /root/lastUpdateTime.flag
    then
        exit 0
    fi
 fi
 
 # unless already calling self, update self and call self unless doing only cgis
 # self-updates are not done when suppressed with notSelf and also not in hgwdev-mode to allow testing of local updateBrowser.sh changes
 # Internal sidenote: if you want hgwdev CGIs and also the current hgwdev update
 # script, do a gbibCoreUpdateBeta+updateBrowser hgwdev
 
 # gbibCoreUpdateBeta ends with -Beta because it is used during beta time, to
 # test the current dev update script The update script itself has only a
 # two-stage release process, beta and final, as the alpha version of the script
 # is on the GBiB of the developer itself.
 # the file /root/gbibSkipUpdate allows to skip one single auto-update
 if [[ ( "$BASH_ARGV" != "notSelf" && "$1" != "hgwdev" ) && ( ! -e /root/gbibSkipNextUpdate ) ]] ; then
     echo getting new update script
     # we got three VMs where updateBrowser.sh was 0 bytes, so doing download/move now
     wget http://hgdownload.soe.ucsc.edu/gbib/updateBrowser.sh -O /root/updateBrowser.sh.new -q && mv /root/updateBrowser.sh.new /root/updateBrowser.sh
     chmod a+x /root/updateBrowser.sh
     /root/updateBrowser.sh $1 notSelf
     exit 0
 fi
 
 rm -f /root/gbibSkipNextUpdate
 
 # check if any hgMirror jobs are running right now
 # check if the group id file exists and also if any processes exist with this group id
 # note that the .pid actually contains a group id, not a process id
 if [ -f /tmp/lastJob.pid ] && [ "$(ps x -o pgid | grep $(cat /tmp/lastJob.pid) | wc -l)" != "0" ] ; then
     echo a hgMirror job is running right now, not updating
     exit 4
 fi
 	
 # --- now do the update ---
 
 # keep a log of all output of this script and the date
 echo --------------------------------- >> $LOGFILE
 date  >> $LOGFILE
 echo --------------------------------- >> $LOGFILE
 exec >> >(tee -a $LOGFILE) 2>&1
 
 # not done, as old customTrash tables will be in innoDb format
 # and can't be read if we deactivate it now
 # deactivate inno-db support in mysql. Saves 400-500MB of RAM.
 #if ! grep skip-innodb /etc/mysql/my.cnf > /dev/null 2> /dev/null ; then
     #echo - Switching off inno-db in /etc/mysql/my.cnf
     #sed -i '/^.mysqld.$/a skip-innodb' /etc/mysql/my.cnf
     #sed -i '/^.mysqld.$/a default-storage-engine=myisam' /etc/mysql/my.cnf
     #service mysql restart
 #fi
    
 # activate the apt repo 'main' and 'universe' so we can install external software
 if ! apt-cache policy r-base | grep "Unable to locate" > /dev/null; then
    if ! grep '^deb http://us.archive.ubuntu.com/ubuntu trusty main universe multiverse$' /etc/apt/sources.list > /dev/null; then
        echo - Activating the main Ubuntu package repository
        echo 'deb http://us.archive.ubuntu.com/ubuntu trusty main universe multiverse' >> /etc/apt/sources.list
    fi
 fi
 
 # activate daily automated security updates with automated reboots
 # automated reboots are strange but probably better than to risk exploits
 # see https://help.ubuntu.com/community/AutomaticSecurityUpdates
 if apt-cache policy unattended-upgrades | grep "Installed: .none." > /dev/null; then
    echo - Activating automated daily Ubuntu security updates
    # from http://askubuntu.com/questions/203337/enabling-unattended-upgrades-from-a-shell-script
    apt-get update
    apt-get install -y unattended-upgrades update-notifier-common
    # update package lists every day
    echo 'APT::Periodic::Update-Package-Lists "1";' > /etc/apt/apt.conf.d/20auto-upgrades
    # do the upgrade every day
    echo 'APT::Periodic::Unattended-Upgrade "1";' >> /etc/apt/apt.conf.d/20auto-upgrades
    # reboot if needed
    echo 'Unattended-Upgrade::Automatic-Reboot "true";' >> /etc/apt/apt.conf.d/20auto-upgrades
    # remove packages not used anymore
    echo 'Unattended-Upgrade::Remove-Unused-Dependencies "true";' >> /etc/apt/apt.conf.d/20auto-upgrades
    # and remove the downloaded tarballs at the end
    echo 'APT::Periodic::AutocleanInterval "1";' >> /etc/apt/apt.conf.d/20auto-upgrades
    /etc/init.d/unattended-upgrades restart
 fi
    
 # unattended security upgrades take a while to start, better to force one right now and show the progress
 # this may lead to an auto-reboot, so let's skip the auto-update of this script for this reboot
 touch /root/gbibSkipNextUpdate
 echo - Applying Ubuntu security updates
 unattended-upgrade -v
 rm -f /root/gbibSkipNextUpdate
 
 # The original GBiB image did not use the Ubuntu Virtualbox guest utils but the
 # ones from VirtualBox in /opt. Fix this now and switch to the Ubuntu guest
 # utilities, so they are updated automatically by the Ubuntu tools
 if apt-cache policy virtualbox-guest-dkms | grep "Installed: .none." > /dev/null; then
     echo - Updating VirtualBox Guest utilities
     apt-get install -y linux-headers-generic 
     apt-get install -y virtualbox-guest-dkms
     apt-get -y autoremove
     /etc/init.d/vboxadd start
 
 fi
 
 # install R for the gtex tracks
 if apt-cache policy r-base-core | grep "Installed: .none." > /dev/null; then
    echo - Installing R
    apt-get update
    apt-get --no-install-recommends install -y r-base-core
    apt-get -y autoremove
 fi
 
 # install imagemagick for the session gallery
 if apt-cache policy imagemagick | grep "Installed: .none." > /dev/null; then
    echo - Installing imagemagick
    apt-get update
    apt-get --no-install-recommends install -y imagemagick
    apt-get -y autoremove
 fi
 
 # install mysql-python for hgGeneGraph, actually cgi-bin/pyLib/hgLib.py
 if apt-cache policy python-mysqldb | grep "Installed: .none." > /dev/null; then
    echo - Installing mysql-python
    apt-get update
    apt-get --no-install-recommends install -y python-mysqldb
    apt-get -y autoremove
 fi
 
 # install curl for checking if we are closer to European or US mirror
 if apt-cache policy curl | grep "Installed: .none." > /dev/null; then
    echo - Installing curl
    apt-get update
    apt-get --no-install-recommends install -y curl
    apt-get -y autoremove
    # make sure that the mysql server is re-configured now
    rm -f /usr/local/apache/trash/registration.txt
 fi
 
 echo
 
 # Feb 2021: cgi-bin and htdocs are now too big for the root partition. Moving both to the data partition:
 if [ ! -L /usr/local/apache/htdocs ] ; then
  rsync -avp /usr/local/apache/htdocs/ /data/htdocs/ && rm -rf /usr/local/apache/htdocs && ln -s /data/htdocs /usr/local/apache/htdocs 
 fi
 if [ ! -L /usr/local/apache/cgi-bin ] ; then
  rsync -avp /usr/local/apache/cgi-bin/ /data/cgi-bin/ && rm -rf /usr/local/apache/cgi-bin && ln -s  /data/cgi-bin /usr/local/apache/cgi-bin
 fi
 
 echo - Updating the genome browser software via rsync:
 
 # CGI-BIN and HTDOCS:
 # the parameter "hgwdev" copies over only the beta/alpha CGIs from hgwdev
 if [ "$1" == "hgwdev" ] ; then
     # note the missing -u option to RSYNC: in hgwdev mode, we want to overwrite everything.
     # On a development machine, the developer might have touched a file
     # for testing. We want to make sure that all local files are overwritten by the 
     # files on hgwdev
     RSYNCOPTS="-ltrvh"
     user=$2
     dirExt=$3
 
     if [ "$user" == "" ]; then
         echo arguments: updateBrowser hgwdev hgwdevUsername cgiDirectoryExtension 
         echo in alpha/beta mode you need to provide a username for the hgwdev login
         echo and a directory extension, the part after /usr/local/apache/cgi-bin-XXX
         echo The extension '"alpha"' is translated to '"no extension"'
         echo example '"updateBrowser hgwdev kent alpha"'
         echo example '"updateBrowser hgwdev hiram beta"'
         exit 5
     fi
 
     if [ "$dirExt" == "alpha" ] ; then
     	cgiExt=""
     	htmlExt="" 
     else
     	cgiExt="-"$dirExt
     	htmlExt="-"$dirExt
     fi
 
     RSYNCAPACHE="$RSYNCOPTS --delete"
 
      # remove a lot of clutter that accumulated in hgwdev's alpha cgi-bin dir
     if [ "$dirExt" == "alpha" ] ; then
       RSYNCAPACHE="$RSYNCAPACHE --exclude ENCODE/**.pdf --exclude *.gz --exclude *.bw --exclude *.bb --exclude *.bam --exclude goldenPath/**.pdf --exclude admin/** --exclude goldenPath/customTracks/** --exclude pubs/** --exclude ancestors/** --exclude training/** --exclude trash --exclude style-public/** --exclude js-public/** --exclude **/edw* --exclude images/mammalPsg/** --exclude **/encodeTestHub* --exclude favicon.ico --exclude folders --exclude ENCODE/** --exclude ENCODE/** --exclude Neandertal/** --exclude gbib/** --exclude generator/** --exclude js-*/** --exclude js/*/* --exclude .\* --exclude x86_64/* --exclude .xauth --exclude .hg.conf --exclude hgHeatmap* --exclude hg.conf --exclude 'hgt/**' --exclude admin/** --exclude images --exclude trash --exclude edw* --exclude visiGeneData/** --exclude crom_dir/ --exclude testp/ --exclude *.exe --exclude *.old --exclude *.tmp --exclude *.bak --exclude test* --exclude hg.conf* --exclude **/hgHeatmap* --exclude ~* --exclude Intronerator** --exclude hgText --exclude hgSubj --exclude gisaid* --exclude nt4.dir --exclude qaPush* --exclude docIdView --exclude ct/ --exclude *.bak --exclude hg.conf* --exclude gsid*/ --exclude *.private --exclude useCount --exclude ~* --exclude lssnp/ --exclude hg.conf.local"
     fi
   
     # remove things that are on hgwdev beta directories but not necessary on the gbib
     if [ "$dirExt" == "beta" ] ; then
       RSYNCAPACHE="$RSYNCAPACHE --exclude favicon*.ico --exclude hg.conf* --exclude ENCODE --exclude *.gz --exclude *.bw --exclude *.bb --exclude *.bam --exclude goldenPath/**.pdf --exclude admin --exclude goldenPath/customTracks --exclude pubs --exclude ancestors --exclude training --exclude trash --exclude .htaccess --exclude htdocs --exclude Neandertal --exclude RNA-img --exclude ebola --exclude encodeDCC --exclude evoFold --exclude geneExtra --exclude js-public --exclude style-public --exclude hgNearData --exclude visiGeneData --exclude visiGene"
     fi
 
     rsync $RSYNCAPACHE $user@hgwdev.soe.ucsc.edu:/usr/local/apache/htdocs${htmlExt}/ /usr/local/apache/htdocs/
     rsync $RSYNCAPACHE $user@hgwdev.soe.ucsc.edu:/usr/local/apache/cgi-bin${cgiExt}/ /usr/local/apache/cgi-bin/
 
     PUSHLOC=$user@hgwdev.soe.ucsc.edu:/usr/local/apache/htdocs/gbib/push/
 
 # normal public updates from hgdownload are easier, not many excludes necessary
 else
 
     # update CGIs
     echo - Updating CGIs...
     rsync --delete -u $RSYNCOPTS $RSYNCSRC/$RSYNCCGIBIN /data/cgi-bin/ --exclude=hg.conf --exclude=hg.conf.local --exclude edw* --exclude *private --exclude hgNearData --exclude visiGeneData --exclude Neandertal 
 
     echo - Updating HTML files...
     # not using -u because we had a case with a 0-byte html page that was 
     # not updated anymore in #18337
     rsync --delete $RSYNCOPTS $RSYNCSRC/$RSYNCHTDOCS/ /data/htdocs/ --include **/customTracks/*.html --exclude ENCODE/ --exclude *.bam --exclude *.bb --exclude */*.bw --exclude */*.gz --exclude favicon.ico --exclude folders --exclude ancestors --exclude admin --exclude goldenPath/customTracks --exclude images/mammalPsg --exclude style/gbib.css --exclude images/title.jpg --exclude images/homeIconSprite.png --exclude goldenPath/**.pdf --exclude training
 
     PUSHLOC=hgdownload.soe.ucsc.edu::gbib/push/
 fi
 
 chown -R www-data.www-data /usr/local/apache/cgi-bin/*
 chown -R www-data.www-data /usr/local/apache/htdocs/
 chmod -R a+r /usr/local/apache/htdocs
 
 # June 2017: add a basic set of hg38 files to the GBIB
 # This will add 1.2 GB to the size of the virtual disc but hg38
 # is the default genome so probably should be included
 # Touching the files once is enough. Rsync will download them.
 mkdir -p /data/gbdb/hg38
 mkdir -p /data/gbdb/hg38/targetDb/
 mkdir -p /data/gbdb/hg38/html/
 mkdir -p /data/mysql/hg38
 
 # GBDB files
 for i in hg38.2bit html/description.html knownGene.ix knownGene.ixx knownGene.bb targetDb/kgTargetSeq10.2bit targetDb/kgTargetSeq8.2bit targetDb/kgTargetSeq9.2bit trackDb.ix trackDb.ixx; do
    touch /data/gbdb/hg38/$i;
 done
 
 # MySQL tables
 for i in chromInfo cytoBand cytoBandIdeo ensemblLift extFile grp gtexGene gtexGeneModel hgFindSpec kgColor kgXref knownCanonical knownGene knownToTag ncbiRefSeq ncbiRefSeqCurated ncbiRefSeqLink ncbiRefSeqOther ncbiRefSeqPredicted ncbiRefSeqPsl refGene tableList trackDb ucscToEnsembl ucscToINSDC xenoRefGene; do
    touch /data/mysql/hg38/$i.MYD;
    touch /data/mysql/hg38/$i.MYI;
    touch /data/mysql/hg38/$i.frm;
 done
 
 # adding tables that are required for gtex, which is now a default track, #19587
 touch /data/mysql/hgFixed/gtexInfo.{MYI,MYD,frm}
 touch /data/mysql/hgFixed/gtexTissue.{MYI,MYD,frm}
 
 # -- END JUNE 2017
 
+# add gtex v8 data, which is now a default track, #27854:
+touch /data/mysql/hg38/gtexGeneModelV8.{MYI,MYD,frm}
+touch /data/mysql/hg38/gtexGeneV8.{MYI,MYD,frm}
+touch /data/mysql/hgFixed/gtexTissueV8.{MYI,MYD,frm}
+
 # Feb 2021, knownCds is required for knownGene display
 for db in hg38 mm10; do
     if [ -e "/data/mysql/$db" ] ; then
        touch /data/mysql/$db/knownCds.{MYI,MYD,frm}
     fi
 done
 
 if [ "$1" != "hgwdev" ] ; then
   echo - Updating GBDB files...
   rsync $RSYNCOPTS --existing rsync://hgdownload.soe.ucsc.edu/gbdb/ /data/gbdb/
   chown -R www-data.www-data /data/gbdb/
 fi
 
 echo - Pulling other files
 # make sure we never overwrite the hg.conf.local file
 # Feb 2021: requires -K now since /usr/local/apache/{cgi-bin,htdocs} are symlinks
 rsync -ltrvhK --exclude=hg.conf.local $PUSHLOC / 
 
 # July 2016: add the cram fetcher to root's crontab 
 # this has to be done after the PUSHLOC directory has been copied over
 if grep -q fetchCramReference /var/spool/cron/crontabs/root; then
         true
    else
        crontab -l | awk '{print} END {print "\n# handle CRAM auto reference download\n*/1 * * * * /root/fetchCramReference.sh /data/cramCache/pending /data/cramCache/ /data/cramCache/error/\n"}' | crontab -   
 fi
 # also create the directories for the cram files
 # cram also requires that the directories are writable by the apache user
 if [ ! -d /data/cramCache ]; then
     mkdir -p /data/cramCache/pending /data/cramCache/error
     chown -R www-data:www-data /data/cramCache
 fi
 # -- end July 2016
 
 # July 2016: genbank tables are now in hgFixed. By touching a few files, we make sure that at least refseqStatus 
 # is rsync'ed later, otherwise gbib is really slow, refs #17842
 touch /data/mysql/hgFixed/refSeqStatus.MYI /data/mysql/hgFixed/refSeqStatus.MYD /data/mysql/hgFixed/refSeqStatus.frm 
 touch /data/mysql/hgFixed/refLink.MYI /data/mysql/hgFixed/refLink.MYD /data/mysql/hgFixed/refLink.frm 
 
 # Jan 2017: hgVai does not work if /data/mysql/hg19/wgEncodeRegTfbsClusteredInputsV3 is not present, so force this 
 # table into the rsync, refs #18778
 touch /data/mysql/hg19/wgEncodeRegTfbsClusteredInputsV3.{frm,MYI,MYD}
 
 # Oct 2019: hg38 does not work if /data/mysql/hg38/knownAttrs is not present, so force this
 # table into the rsync, refs #24398
 touch /data/mysql/hg38/knownAttrs.{frm,MYI,MYD}
 
 # Jun 2017: An Ubuntu security update in early 2017 deactivated LOAD DATA in Mysql
 # so we are switching it back on
 if grep -q secure-file-priv /etc/mysql/my.cnf; then
     true
 else
     echo Allowing LOAD DATA in MySQL and restart MySQL
     sed -i '/\[mysqld\]/a secure-file-priv = ""' /etc/mysql/my.cnf
     service mysql restart
 fi
 
 # we can now remove the old tables
 rm -f /data/mysql/hg19/refSeqStatus*
 
 if [ "$1" != "hgwdev" ] ; then
   echo updating MYSQL files - browser will not work during the MYSQL update
   # inspired by http://forums.mysql.com/read.php?35,45577,47063#msg-47063
   # it doesn't work if I use two mysql invocations, as 'flush tables with read lock'
   # is only valid as long as the session is open
   # so I use the SYSTEM command
   echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync $RSYNCOPTS --existing rsync://hgdownload.soe.ucsc.edu/mysql/ /data/mysql/; SYSTEM chown -R mysql.mysql /data/mysql/; UNLOCK TABLES;" | mysql
   
   echo updating hgcentral database, make sure to always overwrite
   echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync -vrz rsync://hgdownload.soe.ucsc.edu/mysql/hgcentral/ /data/mysql/hgcentral/ --exclude hubSearch* --exclude tableDescriptions* --exclude hubSearchText* --exclude gbNode* --exclude geoIp* ; SYSTEM chown -R mysql.mysql /data/mysql/hgcentral; UNLOCK TABLES;" | mysql
   # update blat servers
   mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".soe.ucsc.edu") WHERE host not like "%ucsc.edu"'
   # the box does not officially support the HAL right now, remove the ecoli hubs
   mysql hgcentral -e 'delete from hubPublic where hubUrl like "%nknguyen%"'
 fi
 
 echo - Adapting the menu 
 cp /usr/local/apache/htdocs/inc/globalNavBar.inc /tmp/navbar.inc
 # remove mirrors and downloads menu
 sed -i '/<li class="menuparent" id="mirrors">/,/^<\/li>$/d' /tmp/navbar.inc 
 sed -i '/<li class="menuparent" id="downloads">/,/^<\/li>$/d' /tmp/navbar.inc 
 # adding the link to the mirror tracks tool
 sed -i '/hgLiftOver/a <li><a href="../cgi-bin/hgMirror">Mirror tracks</a></li>' /tmp/navbar.inc
 # add a link to the gbib shared data folder
 sed -i '/Track Hubs/a <li><a target="_blank" href="\/folders\/">GBiB Shared Data Folder<\/a><\/li>' /tmp/navbar.inc
 # adding a link to the GBIB help pages
 sed -i '/genomewiki/a <li><a href="../goldenPath/help/gbib.html">Help on GBiB</a></li>' /tmp/navbar.inc
 cat /tmp/navbar.inc | grep -v hgNear | grep -v hgVisiGene | uniq > /usr/local/apache/htdocs/inc/globalNavBar.inc
 rm /tmp/navbar.inc
 
 # patch left side menu:
 # remove encode, neandertal, galaxy, visiGene, Downloads, cancer browser, microbial, mirrors, jobs
 for i in hgNear ENCODE Neandertal galaxy VisiGene hgdownload genome-cancer microbes mirror jobs; do
     sed -i '/<A CLASS="leftbar" .*'$i'.*$/,/<HR>$/d' /usr/local/apache/htdocs/index.html
 done
 
 # patch main pages
 sed -i 's/About the UCSC Genome Bioinformatics Site/About the UCSC Genome Browser in a Box/g' /usr/local/apache/htdocs/indexIntro.html
 perl -0777 -pi -e 's/It also.+ provides.+> project. //s' /usr/local/apache/htdocs/indexIntro.html
 perl -0777 -pi -e 's/Program-driven.+ per day.//s' /usr/local/apache/htdocs/indexInfo.html
 # patch contacts page
 sed -i 's/......cgi-bin\/hgUserSuggestion/http:\/\/genome.ucsc.edu\/cgi-bin\/hgUserSuggestion/' /usr/local/apache/htdocs/contacts.html
 # remove visigene from top menu
 sed -i '/hgVisiGene/d' /usr/local/apache/htdocs/inc/home.topbar.html
 
 # maybe not needed, but running anyway
 chown www-data.www-data /usr/local/apache/htdocs/inc/globalNavBar.inc
 
 # make sure we have the right symlink to /media
 sudo ln -sfT /media /usr/local/apache/htdocs/folders
 sudo ln -sfT /data/trash /usr/local/apache/htdocs/trash
 
 # make sure this tableList is not there, it can break the box
 # hgcentral on hgdownload has tables missing: those with users and passwords
 mysql hgcentral -e 'drop table if exists tableList'
 
 # hide the really big tracks
 mysql hg19 -e 'update trackDb set visibility=0 where tableName like "cons%way"'
 mysql hg19 -e 'update trackDb set visibility=0 where tableName like "ucscRetroAli%"'
 
 # temporary fix for hgdownload problem, Oct 2014
 ls /data/mysql/eboVir3 > /dev/null 2> /dev/null && mysql eboVir3 -e 'drop table if exists history'
 
 # rsync tables on hgdownload are sometimes in a crashed state
 echo checking mysql tables
 #sudo myisamchk --force --silent --fast /data/mysql/hg19/*.MYI /data/mysql/hgcentral/*.MYI /data/mysql/hgFixed/*.MYI 2> /dev/null
 mysqlcheck --all-databases --auto-repair --quick --fast --silent
 
 #LATENCY=`ping genome.ucsc.edu -n -c1 -q | grep rtt | cut -d' ' -f4 | cut -d/ -f2 | cut -d. -f1`
 #if [ "$LATENCY" -gt "90" ]; then
 #echo making low-latency changes
 /usr/local/apache/cgi-bin/hgMirror postRsyncUpdates
 
 # the local-only hg.conf settings file has to exist as it is included from hg.conf
 # In case it got deleted due to some error, recreate it
 if [ ! -f /usr/local/apache/cgi-bin/hg.conf.local ] ; then
    echo Creating /usr/local/apache/cgi-bin/hg.conf.local
    echo allowHgMirror=true > /usr/local/apache/cgi-bin/hg.conf.local
 fi
 
 # Sept 2017: check if genome-euro mysql server is closer
 if [ ! -f /usr/local/apache/trash/registration.txt ]; then
    # Mar 2018:  check if we can connect to genome-euro before checking what is closest
    curl -sSI genome-euro.ucsc.edu 2>&1 > /dev/null
    if [[ $? -eq 0 ]]; then
       echo comparing latency: genome.ucsc.edu Vs. genome-euro.ucsc.edu
       euroSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome-euro.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       ucscSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       if [[ $(awk '{if ($1 <= $2) print 1;}' <<< "$euroSpeed $ucscSpeed") -eq 1 ]]; then
          echo genome-euro seems to be closer
          echo modifying gbib to pull data from genome-euro instead of genome
          sed -i s/slow-db.host=genome-mysql.soe.ucsc.edu/slow-db.host=genome-euro-mysql.soe.ucsc.edu/ /usr/local/apache/cgi-bin/hg.conf
          # Nov 2018: hgdownload-euro is online now
          sed -i 's#gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/#gbdbLoc2=http://hgdownload-euro.soe.ucsc.edu/gbdb/#' /usr/local/apache/cgi-bin/hg.conf
       else
          echo genome.ucsc.edu seems to be closer
          echo not modifying /usr/local/apache/cgi-bin/hg.conf
       fi
    fi
 fi
 
 touch /root/lastUpdateTime.flag
 echo - GBiB update done
 cat /etc/issue | tr -s '\n'