diff --git a/Makefile b/Makefile
index 6eb6c69..d20b64c 100644
--- a/Makefile
+++ b/Makefile
@@ -82,7 +82,7 @@ $(call singleton,$(TARGETS_cellprofiler)) : $(SOURCES_cellprofiler_headless)
 	$(PARALLEL) :::: $<
 
 $(TARGETS_cellprofiler_commands) : $(SOURCES_cellprofiler_commands)
-	$(CELLPROFILER) --get-batch-commands=$< | sed 's#^CellProfiler#$(CELLPROFILER)#' > $@
+	$(CELLPROFILER) --get-batch-commands=$< | sed 's#^CellProfiler#$(CELLPROFILER)#' | sort -nk 8.14 > $@
 
 $(TARGETS_cellprofiler_batch) : $(SOURCES_cellprofiler)
 	$(CELLPROFILER) $(CELLPROFILER_OPTS) --run-headless