630ec442be94b7101d52477cbebf06d66633427f
braney
  Wed Feb 24 14:56:34 2021 -0800
add fonts to GBiB

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index 1665054..6478ddf 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -412,31 +412,31 @@
     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 --existing rsync://hgdownload.soe.ucsc.edu/mysql/hgcentral/ /data/mysql/hgcentral/; SYSTEM chown -R mysql.mysql /data/mysql/hgcentral; UNLOCK TABLES;" | mysql
+  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