diff --git a/data/bootstrap/mysql-db-dir.tbz b/data/bootstrap/mysql-db-dir.tbz
index 9687720c0b..311b1ed7f7 100644
Binary files a/data/bootstrap/mysql-db-dir.tbz and b/data/bootstrap/mysql-db-dir.tbz differ
diff --git a/data/bootstrap/mysql-db-dir_10.0.10-MariaDB.tbz b/data/bootstrap/mysql-db-dir_10.0.10-MariaDB.tbz
deleted file mode 100644
index 27b91bc389..0000000000
Binary files a/data/bootstrap/mysql-db-dir_10.0.10-MariaDB.tbz and /dev/null differ
diff --git a/data/bootstrap/mysql-db-dir_10.0.13-MariaDB.tbz b/data/bootstrap/mysql-db-dir_10.0.13-MariaDB.tbz
new file mode 100644
index 0000000000..3baf037335
Binary files /dev/null and b/data/bootstrap/mysql-db-dir_10.0.13-MariaDB.tbz differ
diff --git a/data/bootstrap/upgrade.sh b/data/bootstrap/upgrade.sh
index a64a8c216d..241b52a5e9 100755
--- a/data/bootstrap/upgrade.sh
+++ b/data/bootstrap/upgrade.sh
@@ -8,24 +8,25 @@ if [ -z "$VTDATAROOT" ]; then
   exit 1
 fi
 
+mysql_port=33306
 tablet_uid=99999
 tablet_dir=$VTDATAROOT/vt_0000099999
 
 set -e
 
 echo Starting mysqld
-mysqlctl -tablet_uid=$tablet_uid init -skip_schema
+mysqlctl -tablet_uid=$tablet_uid -mysql_port=$mysql_port init -skip_schema
 
 echo Running mysql_upgrade
 mysql_upgrade --socket=$tablet_dir/mysql.sock --user=vt_dba 
 
 echo Stopping mysqld
-mysqlctl -tablet_uid=$tablet_uid shutdown
+mysqlctl -tablet_uid=$tablet_uid -mysql_port=$mysql_port shutdown
 
 newfile=mysql-db-dir_$(cat $tablet_dir/data/mysql_upgrade_info).tbz
 
 echo Creating new bootstrap file: $newfile
-(cd $tablet_dir/data && tar -jcf ../data.tbz *)
+(cd $tablet_dir && tar -jcf data.tbz data innodb)
 mv $tablet_dir/data.tbz ./$newfile
 
 echo Removing tablet directory
diff --git a/go/vt/mysqlctl/mysqld.go b/go/vt/mysqlctl/mysqld.go
index 517a8a69e4..3939e0edb8 100644
--- a/go/vt/mysqlctl/mysqld.go
+++ b/go/vt/mysqlctl/mysqld.go
@@ -266,7 +266,7 @@ func (mysqld *Mysqld) Init(mysqlWaitTime time.Duration, bootstrapArchive string,
 	// Unpack bootstrap DB files.
 	dbTbzPath := path.Join(root, "data/bootstrap/"+bootstrapArchive)
 	log.Infof("decompress bootstrap db %v", dbTbzPath)
-	args := []string{"-xj", "-C", mysqld.config.DataDir, "-f", dbTbzPath}
+	args := []string{"-xj", "-C", mysqld.TabletDir, "-f", dbTbzPath}
 	if _, err = execCmd("tar", args, []string{}, ""); err != nil {
 		log.Errorf("failed unpacking %v: %v", dbTbzPath, err)
 		return err
diff --git a/test/mysql_flavor.py b/test/mysql_flavor.py
index a408d38ce6..3ee1a9b776 100644
--- a/test/mysql_flavor.py
+++ b/test/mysql_flavor.py
@@ -62,7 +62,7 @@ class MariaDB(MysqlFlavor):
     return environment.vttop + "/config/mycnf/master_mariadb.cnf"
 
   def bootstrap_archive(self):
-    return "mysql-db-dir_10.0.10-MariaDB.tbz"
+    return "mysql-db-dir_10.0.13-MariaDB.tbz"
 
 
 if environment.mysql_flavor == "MariaDB":