08dfa19bf3032887f066c3ab8943afef74fb8bee
max
  Fri Jun 9 14:50:41 2017 -0700
fixing hg38 mysql update in gbib, refs #19587

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index b15de9e..198dfea 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -305,42 +305,43 @@
     rsync --delete $RSYNCOPTS $RSYNCSRC/$RSYNCHTDOCS/ /usr/local/apache/htdocs/ --include **/customTracks/*.html --exclude ENCODE/ --exclude *.bam --exclude *.bb --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 --exclude goldenPath/**.pdf --exclude training
 
     PUSHLOC=hgdownload.cse.ucsc.edu::gbib/push/
 fi
 
 chown -R www-data.www-data /usr/local/apache/cgi-bin/*
 chown -R www-data.www-data /usr/local/apache/htdocs/
 chmod -R a+r /usr/local/apache/htdocs
 
 # June 2017: add a basic set of hg38 files to the GBIB
 # This will add 1.2 GB to the size of the virtual disc but hg38
 # is the default genome so probably should be included
 # Touching the files once is enough. Rsync will download them.
 mkdir -p /data/gbdb/hg38
 mkdir -p /data/gbdb/hg38/targetDb/
+mkdir -p /data/gbdb/hg38/html/
 mkdir -p /data/mysql/hg38
 
 # GBDB files
 for i in hg38.2bit html/description.html knownGene.ix knownGene.ixx knownGene.bb targetDb/kgTargetSeq10.2bit targetDb/kgTargetSeq8.2bit targetDb/kgTargetSeq9.2bit trackDb.ix trackDb.ixx; do
    touch /data/gbdb/hg38/$i;
 done
 
 # MySQL tables
 for i in chromInfo cytoBand cytoBandIdeo ensemblLift extFile grp gtexGene gtexGeneModel hgFindSpec kgColor kgXref knownCanonical knownGene knownToTag ncbiRefSeq ncbiRefSeqCurated ncbiRefSeqLink ncbiRefSeqOther ncbiRefSeqPredicted ncbiRefSeqPsl refGene tableList trackDb ucscToEnsembl ucscToINSDC xenoRefGene; do
-   touch /data/mysql/$i.MYD;
-   touch /data/mysql/$i.MYI;
-   touch /data/mysql/$i.frm;
+   touch /data/mysql/hg38/$i.MYD;
+   touch /data/mysql/hg38/$i.MYI;
+   touch /data/mysql/hg38/$i.frm;
 done
 # -- END JUNE 2017
 
 if [ "$1" != "hgwdev" ] ; then
   echo - Updating GBDB files...
   rsync $RSYNCOPTS --existing rsync://hgdownload.cse.ucsc.edu/gbdb/ /data/gbdb/
   chown -R www-data.www-data /data/gbdb/
 fi
 
 echo - Pulling other files
 # make sure we never overwrite the hg.conf.local file
 rsync $RSYNCOPTS $PUSHLOC / --exclude=hg.conf.local
 
 # July 2016: add the cram fetcher to root's crontab 
 # this has to be done after the PUSHLOC directory has been copied over
@@ -359,31 +360,31 @@
 
 # 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 
 
 # Jan 2017: hgVai does not work if /data/mysql/hg19/wgEncodeRegTfbsClusteredInputsV3 is not present, so force this 
 # table into the rsync, refs #18778
 touch /data/mysql/hg19/wgEncodeRegTfbsClusteredInputsV3.{frm,MRI,MYD}
 
 # Jun 2017: An Ubuntu security update in early 2017 deactivated LOAD DATA in Mysql
 # so we are switching it back on
 if grep -q secure-file-priv /etc/mysql/my.cnf; then
     true
 else
-    echo Allowing LOAD DATA in MySQL again and restarat MySQL
+    echo Allowing LOAD DATA in MySQL and restart MySQL
     sed -i '/\[mysqld\]/a secure-file-priv = ""' /etc/mysql/my.cnf
     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.cse.ucsc.edu/mysql/ /data/mysql/; SYSTEM chown -R mysql.mysql /data/mysql/; UNLOCK TABLES;" | mysql