102acb1e520a68eed9cca59f1a39a0cfc3de84ab
max
  Fri Aug 5 14:57:31 2016 -0700
fixing gbib speed problem after refseq change, refs #17842

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index 9203fd3..c3cc641 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -312,30 +312,37 @@
 # 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 
+# 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.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