diff --git a/src/ci/run.sh b/src/ci/run.sh
index e3f38e4834a..afa6d1fa0ae 100755
--- a/src/ci/run.sh
+++ b/src/ci/run.sh
@@ -105,7 +105,15 @@ fi
 travis_fold end log-system-info
 
 if [ ! -z "$SCRIPT" ]; then
-  sh -x -c "$SCRIPT"
+  # FIXME(#49246): Re-enable these tools after #49246 has been merged and thus fixing the cache.
+  if [ "$DEPLOY_ALT" = 1 ]; then
+    sh -x -c "$SCRIPT \
+       --exclude src/tools/rls \
+       --exclude src/tools/rustfmt \
+       --exclude src/tools/clippy"
+  else
+    sh -x -c "$SCRIPT"
+  fi
 else
   do_make() {
     travis_fold start "make-$1"