a93a919407cb6f0692c00c122f8dc13335fc9630
max
  Tue Oct 17 09:02:26 2023 -0700
hiding OMIM track on GBIB to avoid error in offline mode and also
adding /gbdb symlink to make sure that v455 doesn't cause trouble on
GBIB. refs #32440

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index dde0681..42f466f 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -515,30 +515,32 @@
 
 # maybe not needed, but running anyway
 chown www-data.www-data /usr/local/apache/htdocs/inc/globalNavBar.inc
 
 # make sure we have the right symlink to /media
 sudo ln -sfT /media /usr/local/apache/htdocs/folders
 sudo ln -sfT /data/trash /usr/local/apache/htdocs/trash
 
 # make sure this tableList is not there, it can break the box
 # hgcentral on hgdownload has tables missing: those with users and passwords
 mysql hgcentral -e 'drop table if exists tableList'
 
 # hide the really big tracks
 mysql hg19 -e 'update trackDb set visibility=0 where tableName like "cons%way"'
 mysql hg19 -e 'update trackDb set visibility=0 where tableName like "ucscRetroAli%"'
+mysql hg38 -e 'update trackDb set visibility=0 where tableName like "omimGene2"'
+mysql hg19 -e 'update trackDb set visibility=0 where tableName like "omimGene2"'
 
 # temporary fix for hgdownload problem, Oct 2014
 ls /data/mysql/eboVir3 > /dev/null 2> /dev/null && mysql eboVir3 -e 'drop table if exists history'
 
 # rsync tables on hgdownload are sometimes in a crashed state
 echo checking mysql tables
 #sudo myisamchk --force --silent --fast /data/mysql/hg19/*.MYI /data/mysql/hgcentral/*.MYI /data/mysql/hgFixed/*.MYI 2> /dev/null
 mysqlcheck --all-databases --auto-repair --quick --fast --silent
 
 #LATENCY=`ping genome.ucsc.edu -n -c1 -q | grep rtt | cut -d' ' -f4 | cut -d/ -f2 | cut -d. -f1`
 #if [ "$LATENCY" -gt "90" ]; then
 #echo making low-latency changes
 /usr/local/apache/cgi-bin/hgMirror postRsyncUpdates
 
 # the local-only hg.conf settings file has to exist as it is included from hg.conf
@@ -557,18 +559,22 @@
       euroSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome-euro.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       ucscSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       if [[ $(awk '{if ($1 <= $2) print 1;}' <<< "$euroSpeed $ucscSpeed") -eq 1 ]]; then
          echo genome-euro seems to be closer
          echo modifying gbib to pull data from genome-euro instead of genome
          sed -i s/slow-db.host=genome-mysql.soe.ucsc.edu/slow-db.host=genome-euro-mysql.soe.ucsc.edu/ /usr/local/apache/cgi-bin/hg.conf
          # Nov 2018: hgdownload-euro is online now
          sed -i 's#gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/#gbdbLoc2=http://hgdownload-euro.soe.ucsc.edu/gbdb/#' /usr/local/apache/cgi-bin/hg.conf
       else
          echo genome.ucsc.edu seems to be closer
          echo not modifying /usr/local/apache/cgi-bin/hg.conf
       fi
    fi
 fi
 
+# Oct 2023: a bug in release 455 (fixed for 456) means that GBIB must have a /gbdb directory, not /data/gbdb. 
+# Adding this symlink now.
+ln -sf /data/gbdb /gbdb
+
 touch /root/lastUpdateTime.flag
 echo - GBiB update done
 cat /etc/issue | tr -s '\n'