diff --git a/apps/Makefile b/apps/Makefile
index 6cea5268d..c27cc6465 100644
--- a/apps/Makefile
+++ b/apps/Makefile
@@ -11,6 +11,25 @@ apps =
 # (path to the apps header).
 $(foreach i,${apps_list},${eval include apps/$(i)/Makefile})
 
+app_equals = $(and $(findstring $(1),$(2)),$(findstring $(2),$(1)))
+# We list all the apps that are missing
+apps_missing = $(foreach i, ${apps_list}, $(if $(call app_equals, apps/$(i)/Makefile, $(wildcard apps/$(i)/Makefile)),, $(i) ) )
+
+# If the two doesn't match, we got an error.
+ifneq ($(strip $(apps_missing)),)
+    miss_modules = 0
+
+    # Check if the missing apps are one that are supposed to be submodules
+    $(foreach i, $(SUBMODULES_APPS), $(if $(call app_equals, $(filter $(i), $(apps_missing)), $(i)), $(eval miss_modules=1)))
+
+    ifeq ($(miss_modules), 1)
+        PLS_IGNORE := $(shell >&2 printf "\nSome submodules apps seem to be missing. To download them, assumming you git clone'd the repo, do\n")
+        PLS_IGNORE := $(shell >&2 printf "  git submodule init\n")
+        PLS_IGNORE := $(shell >&2 printf "  git submodule update\n\n")
+    endif
+    $(error Missing apps: $(strip $(apps_missing)))
+endif
+
 apps_src += $(addprefix apps/,\
   alternate_empty_nested_menu_controller.cpp \
   apps_container.cpp \
diff --git a/build/config.mak b/build/config.mak
index dd0354e16..285dc9bf1 100644
--- a/build/config.mak
+++ b/build/config.mak
@@ -9,6 +9,7 @@ OMEGA_VERSION ?= 1.21.0
 # OMEGA_USERNAME ?= N/A
 OMEGA_STATE ?= dev
 EPSILON_APPS ?= calculation rpn graph code statistics probability solver atom sequence regression settings external
+SUBMODULES_APPS = atom rpn
 EPSILON_I18N ?= en fr nl pt it de es hu
 EPSILON_COUNTRIES ?= WW CA DE ES FR GB IT NL PT US
 EPSILON_GETOPT ?= 0