a9aec4b359d86fc7d9662b8bdcb7e61828093e9b
max
  Tue Nov 2 06:18:18 2021 -0700
moving BLAT tools into main bin directory in GBIB and GBIC, refs #28435

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index 06738c3..bba907d 100755
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -1772,30 +1772,31 @@
 
    # update the mysql DBs
    stopMysql
    DBS=`ls /var/lib/mysql/ | egrep -v '(Trash$)|(hgTemp)|(^ib_)|(^ibdata)|(^aria)|(^mysql)|(performance)|(.flag$)|(hgcentral)'`
    for db in $DBS; do 
        echo2 syncing full mysql database: $db
        $RSYNC --update --progress -avp $RSYNCOPTS $HGDOWNLOAD::mysql/$db/ $MYSQLDIR/$db/
    done
    startMysql
 
    echo2 update finished
 }
 
 function addTools {
    rsync -avP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ /usr/local/bin/
+   mv /usr/local/bin/blat/* /usr/local/bin/ # tools under the BLAT license are separated into their own directory
    echo2 The UCSC User Tools were copied to /usr/local/bin
    echo2 Please note that most of the tools require an .hg.conf file in the users
    echo2 home directory. A very minimal .hg.conf file can be found here:
    echo2 "http://genome-source.soe.ucsc.edu/gitlist/kent.git/blob/master/src/product/minimal.hg.conf"
 }
 
 # ------------ end of utility functions ----------------
 
 # -- START OF SCRIPT  --- MAIN ---
 
 # On Debian and OSX, sudo by default does not update the HOME variable (hence the -H option above)
 if [[ "${SUDO_USER:-}" != "" ]]; then
    export HOME=~root
 fi