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'