diff --git a/run.sh b/run.sh
index 9746f62b3720..730087915589 100755
--- a/run.sh
+++ b/run.sh
@@ -43,10 +43,6 @@ then
     export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
 fi
 
-if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
-    python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
-fi
-
 set_galaxy_config_file_var
 
 if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
diff --git a/run_reports.sh b/run_reports.sh
index 4c1e3c16db8c..e5b9158723cb 100755
--- a/run_reports.sh
+++ b/run_reports.sh
@@ -35,10 +35,6 @@ if [ -z "$GALAXY_REPORTS_CONFIG" ]; then
     export GALAXY_REPORTS_CONFIG
 fi
 
-if [ -n "$GALAXY_REPORTS_CONFIG_DIR" ]; then
-    python ./scripts/build_universe_config.py "$GALAXY_REPORTS_CONFIG_DIR" "$GALAXY_REPORTS_CONFIG"
-fi
-
 find_server ${GALAXY_REPORTS_CONFIG:-none} reports
 echo "Executing: $run_server $server_args"
 eval $run_server $server_args