6ff718895af1691a63eb4472f75659882e6df3ad
max
  Thu Oct 9 04:33:43 2014 -0700
various changes to gbib config files
diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
new file mode 100755
index 0000000..4dcc2c6
--- /dev/null
+++ src/browserbox/root/updateBrowser.sh
@@ -0,0 +1,179 @@
+#!/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 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
+    #echo update already running
+    exit 1
+fi
+	
+# use the right update script, depending on version
+if [ "$1" == "alpha" -o "$1" == "beta" -o "$1" == "devbox" ] ; then
+    # the alpha/beta/devbox states always overwrite even if files are newer
+    # note the missing -u option
+    RSYNCOPTS="-ltrzvh"
+    UPDATEBASE=http://hgwdev.soe.ucsc.edu/gbib
+    UPDATEFLAG=http://hgwdev.soe.ucsc.edu/gbib/lastUpdate
+else
+    UPDATEBASE=http://hgdownload.cse.ucsc.edu/gbib
+    UPDATEFLAG=http://hgdownload.cse.ucsc.edu/gbib/lastUpdate
+fi
+
+# check flag if run with no parameter (=from cron)
+if [ "$#" -eq 0 ] ; then
+   # check a flag file to see if anything on hgdownload actually changed
+   if /root/urlIsNotNewerThanFile $UPDATEFLAG /root/lastUpdateTime.flag
+   then
+       exit 0
+   fi
+fi
+
+# unless already calling self, update self and call self
+if [ "$BASH_ARGV" != "noUpdate" ] ; then
+    echo getting new update script
+    # we got three VMs where updateBrowser.sh was 0 bytes, so doing download/move now
+    wget $UPDATEBASE/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 $1 noUpdate
+    exit 0
+fi
+
+# check if any hgMirror jobs are running right now
+# check if the group id file exists and also if any processes exist with this group id
+# note that the .pid actually contains a group id, not a process id
+if [ -f /tmp/lastJob.pid ] && [ "$(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.