c0d9f279ee53ddada2a13507927fdca11fa85e8f
max
  Thu Sep 24 06:58:37 2015 -0700
make gbib update script avoid errors if not running on virtualbox. no
redmine. based on email by Carsten Kuenne via Bob.

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index d38ae76..d17ddea 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -50,34 +50,36 @@
 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
     #echo update already running
     exit 2
 fi
 	
-# check if auto-updates were deactivated from the Vbox host via a property
+# check if we're on VBox and if yes, if auto-updates were deactivated from the Vbox host via a property
+if which VBoxControl > /dev/null; then
    if VBoxControl guestproperty get gbibAutoUpdateOff | grep -xq "Value: yes" ; then
        exit 6
    fi
+fi
 
 # check if we have internet
 wget -q --tries=1 --timeout=10 --spider http://hgdownload.soe.ucsc.edu -O /dev/null
 if [ $? -ne 0 ] ; then
     exit 3
 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
@@ -184,32 +186,30 @@
   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, make sure to always overwrite
   echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync -vrz --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") 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 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 
-# add a link to the gbib shared data folder
-sed -i '/Track Hubs/a          <li><a href="http:\/\/127.0.0.1:1234\/folders\/">GBiB Shared Data Folder<\/a><\/li>' /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.+> 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