82e124d638bd74bc879bbf919232ecfb21aa2405
max
  Tue Jan 4 08:38:31 2022 -0800
Updating Dockerfile to Ubuntu 20. This brought up a small bug in GBIC which is fixed now. Also updating the Dockerfile docs. Next step is to build the image on hgwdev with the build and upload the image to Docker hub. refs #28585 and hopefully a new ticket at some point for better Docker support.

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index af39aa2..0f33790 100755
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -510,30 +510,31 @@
 function setMYCNF ()
 {
     if [ -f /etc/my.cnf ] ; then
 	# Centos 6-8
     	MYCNF=/etc/my.cnf
     elif [ -f /etc/mysql/my.cnf ] ; then
         # Ubuntu 14
     	MYCNF=/etc/mysql/my.cnf
     elif [ -f /etc/mysql/mysql.conf.d/mysqld.cnf ] ; then
 	# Ubuntu 16, 18, 20
     	MYCNF=/etc/mysql/mysql.conf.d/mysqld.cnf
     else
     	echo Could not find my.cnf. Adapt 'setMYCNF()' in browserSetup.sh and/or contact us.
     	exit 1
     fi
+    echo Found Mariadb config file: $MYCNF
 }
 
 function mysqlAllowOldPasswords
 # mysql >= 8 does not allow the old passwords anymore. But our client is still compiled
 # with the old, non-SHA256 encryption. So we must deactivate this new feature.
 # What will MariaDB do?
 {
 echo2 'Checking for Mysql version >= 8'
 
 MYSQLMAJ=`mysql -e 'SHOW VARIABLES LIKE "version";' -NB | cut -f2 | cut -d. -f1`
 setMYCNF
 if [ "$MYSQLMAJ" -ge 8 ] ; then
     echo2 'Mysql >= 8 found, checking if default-authentication allows native passwords'
     if grep -q default-authentication $MYCNF; then
         echo2 "default-authentication already set in $MYCNF"
@@ -1238,31 +1239,30 @@
        # centos 7 seems to have another config file for this
        if [ -f /etc/selinux/config ]; then
            sed -i 's/^SELINUX=enforcing/SELINUX=disabled/g' /etc/selinux/config
        fi
     fi
 fi
 }
 
 # setup the mysql databases for the genome browser and grant 
 # user access rights
 function mysqlDbSetup ()
 {
     # -------------------
     # Mysql db setup
     # -------------------
-    mysqlAllowOldPasswords
 
     echo2
     echo2 Creating Mysql databases customTrash, hgTemp and hgcentral
     waitKey
     $MYSQL -e 'CREATE DATABASE IF NOT EXISTS customTrash;'
     $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgcentral;'
     $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgTemp;'
     $MYSQL -e 'CREATE DATABASE IF NOT EXISTS hgFixed;' # empty db needed for gencode tracks
 
     updateBlatServers
     
     echo2
     echo2 "Will now grant permissions to browser database access users:"
     echo2 "User: 'browser', password: 'genome' - full database access permissions"
     echo2 "User: 'readonly', password: 'access' - read only access for CGI binaries"
@@ -1357,30 +1357,32 @@
     # -----  OS - SPECIFIC part -----
     if [ ! -f $COMPLETEFLAG ]; then
        if [[ "$DIST" == "OSX" ]]; then
           installOsx
        elif [[ "$DIST" == "debian" ]]; then
           installDebian
        elif [[ "$DIST" == "redhat" ]]; then
           installRedhat
        fi
     fi
     # OS-specific mysql/apache installers can SET_MYSQL_ROOT to 1 to request that the root
     # mysql user password be changed
 
     # ---- END OS-SPECIFIC part -----
 
+    mysqlAllowOldPasswords
+
     if [[ "${SET_MYSQL_ROOT}" == "1" ]]; then
        mysqlChangeRootPwd
     fi
 
     # Ideally, setup modern R fonts like at UCSC:
     # Rscript -e "install.packages(c('showtext', 'curl'), repos='http://cran.us.r-project.org')
 
     # before we do anything else with mysql
     # we need to check if we can access it. 
     # so test if we can connect to the mysql server
     checkCanConnectMysql
 
     disableSelinux
 
     checkDownloadUdr