de291077a84ac6096e26788998369aa1cad5320f
chmalee
  Mon Feb 1 16:34:16 2021 -0800
Fixing missing knownCds table on gbibs, refs #26781

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index a513785..f602355 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -336,30 +336,33 @@
 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/hg38/$i.MYD;
    touch /data/mysql/hg38/$i.MYI;
    touch /data/mysql/hg38/$i.frm;
 done
 
 # adding tables that are required for gtex, which is now a default track, #19587
 touch /data/mysql/hgFixed/gtexInfo.{MYI,MYD,frm}
 touch /data/mysql/hgFixed/gtexTissue.{MYI,MYD,frm}
 
 # -- END JUNE 2017
 
+# Feb 2021, knownCds is required for knownGene display
+touch /data/mysql/hg38/knownCds.{MYI,MYD,frm}
+
 if [ "$1" != "hgwdev" ] ; then
   echo - Updating GBDB files...
   rsync $RSYNCOPTS --existing rsync://hgdownload.soe.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
 if grep -q fetchCramReference /var/spool/cron/crontabs/root; then
         true
    else