b95d8d56dd373541a19a89e17becd2176c3e0ab8 max Mon Oct 6 04:47:04 2014 -0700 gbib update to ubuntu 14 , refs #11957 diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh deleted file mode 100755 index 323fdd7..0000000 --- src/browserbox/root/updateBrowser.sh +++ /dev/null @@ -1,175 +0,0 @@ -#!/bin/bash - -# update script on the box -# - updates itself from hgwdev and then run itself -# - updates cgis, html and gbdb via rsync -# - updates hg.conf via wget -# - patches the menu -# - hides conservation+retro -# - removes some searches if latency to UCSC is > 90msecs - -# will not run if: -# - not run as root -# - if a script named updateBrowser.sh already is running -# - any hgMirror jobs are running -# - if a flagFile on hgDownload is not more recent than a local flag file - - - -# rsync options: -# t = preserve time -# l = preserve symlinks -# p = preserve permissions -# r = recurse -# v = verbose -# z = compress -# P = permit partial download (for restart) -# h = human readable -# u = skip if file is newer on receiver -RSYNCOPTS="-ltrzvhu" -# rsync server for CGIs and html files -RSYNCSRC="rsync://hgdownload.cse.ucsc.edu" -RSYNCCGIBIN=cgi-bin -RSYNCHTDOCS=htdocs - -# check if running as root -if [ "$(id -u)" != "0" ] ; then - echo "This script must be run as root" 1>&2 - exit 1 -fi - -# check flag if run with no parameter (=from cron) -if [ "$#" -eq 0 ] ; then - # check a flag file to see if anything on hgdownload actually changed - if /root/urlIsNotNewerThanFile http://hgdownload.cse.ucsc.edu/gbib/lastUpdate /root/lastUpdateTime.flag - then - exit 0 - fi -fi - -# use the right update script, depending on version -if [ "$1" == "alpha" -o "$1" == "beta" -o "$1" == "devbox" ] ; then - # the alpha/beta/devbox states always overwrite even if files are newer - # note the missing -u option - RSYNCOPTS="-ltrzvh" - UPDATEBASE=http://hgwdev.soe.ucsc.edu/gbib -else - UPDATEBASE=http://hgdownload.cse.ucsc.edu/gbib -fi - -# unless already calling self, update self and call self -if [ "$BASH_ARGV" != "noUpdate" ] ; then - echo getting new update script - wget $UPDATEBASE/updateBrowser.sh -O /root/updateBrowser.sh -q - sudo /root/updateBrowser.sh $1 noUpdate - exit 0 -fi - -# check if running already, 3 = the main script + its update + the outer shell -RUNNING=`ps --no-headers -CupdateBrowser.sh | wc -l` -if [ ${RUNNING} -gt 3 ] ; then - echo already running - exit 1 -fi - -# check if any hgMirror jobs are running right now -# check if the group id file exists and also if any processes exist with this group id -# note that the .pid actually contains a group id, not a process id -if [ -f /tmp/lastJob.pid ] && [ "$(ps x -o pgid | grep $(cat /tmp/lastJob.pid) | wc -l)" != "0" ] ; then - echo a hgMirror job is running right now, not updating - exit 1 -fi - -echo -echo Now updating the genome browser software and data: - -# alpha states cannot use rsync on hgwdev, need to use tarball -if [ "$1" == "alpha" -o "$1" == "beta" -o "$1" == "devbox" ] ; then - echo updating from prepared $1-package on genome-test - pushd . > /dev/null - cd /usr/local/apache - wget http://genome-test.soe.ucsc.edu/browserbox/$1.tgz -O - | tar xvz - cd / - wget http://genome-test.soe.ucsc.edu/browserbox/$1-push.tgz -O - | tar xvz - popd -# normal updates go via rsync -else - # update CGIs - echo updating CGIs... - rsync --delete $RSYNCOPTS $RSYNCSRC/$RSYNCCGIBIN /usr/local/apache/cgi-bin/ --exclude=hg.conf --exclude edw* --exclude *private --exclude hgNearData/** - - echo updating HTML files... - rsync --delete $RSYNCOPTS $RSYNCSRC/$RSYNCHTDOCS/ /usr/local/apache/htdocs/ --include **/customTracks/*.html --exclude ENCODE/ --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 -fi - -chown -R www-data.www-data /usr/local/apache/cgi-bin/* -chown -R www-data.www-data /usr/local/apache/htdocs/ - -echo updating GBDB files... -rsync $RSYNCOPTS --existing rsync://hgdownload.cse.ucsc.edu/gbdb/ /data/gbdb/ -chown -R www-data.www-data /data/gbdb/ - -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.cse.ucsc.edu/mysql/ /data/mysql/; SYSTEM chown -R mysql.mysql /data/mysql/; UNLOCK TABLES;" | mysql - -echo updating hgcentral database -echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync $RSYNCOPTS --existing rsync://hgdownload.cse.ucsc.edu/mysql/hgcentral/ /data/mysql/hgcentral/; SYSTEM chown -R mysql.mysql /data/mysql/hgcentral; UNLOCK TABLES;" | mysql -# update blat servers -mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".cse.ucsc.edu")' -# the box does not support HAL right now, remove the ecoli hubs -mysql hgcentral -e 'delete from hubPublic where hubUrl like "%nknguyen%"' - -echo pulling other files -rsync $RSYNCOPTS hgdownload.cse.ucsc.edu::gbib/push/ / - -echo patching menu -cp /usr/local/apache/htdocs/inc/globalNavBar.inc /tmp/navbar.inc -# remove mirrors and downloads menu -sed -i '/<li class="menuparent" id="mirrors">/,/^<\/li>$/d' /tmp/navbar.inc -sed -i '/<li class="menuparent" id="downloads">/,/^<\/li>$/d' /tmp/navbar.inc -cat /tmp/navbar.inc | grep -v hgNear | grep -v hgVisiGene | sed -e '/hgLiftOver/a <li><a href="../cgi-bin/hgMirror">Mirror tracks</a></li>' | uniq > /usr/local/apache/htdocs/inc/globalNavBar.inc -rm /tmp/navbar.inc - -# patch left side menu: -# remove encode, neandertal, galaxy, visiGene, Downloads, cancer browser, microbial, mirrors, jobs -for i in hgNear ENCODE Neandertal galaxy VisiGene hgdownload genome-cancer microbes mirror jobs; do - sed -i '/<A CLASS="leftbar" .*'$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.+> projects. //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 - -# 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 - -# make sure this tableList is not there, it can break the box -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%"' - -# rsync tables on hgdownload are sometimes a in crashed state -echo checking mysql tables -sudo myisamchk --force --silent --fast --update-state /data/mysql/hg19/*.MYI /data/mysql/hgcentral/*.MYI /data/mysql/hgFixed/*.MYI 2> /dev/null - -#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 - -touch /root/lastUpdateTime.flag -echo update done.