diff --git a/build_tools/gather_sources.py b/build_tools/gather_sources.py
index 85d7d43..d3008a4 100644
--- a/build_tools/gather_sources.py
+++ b/build_tools/gather_sources.py
@@ -141,7 +141,9 @@ def analyze_tree(prefix, t):
     ename = entry.name
     if ename == 'external' or ename == 'zobov':
       continue
-    if type(entry) == Tree:
+    if type(entry) == Submodule:
+      continue
+    elif type(entry) == Tree:
       analyze_tree(prefix + "/" + ename, entry)
     elif type(entry) == Blob:
       if ename == './src/hdf5_flash.h' or ename == './src/h5_readFlash.cpp' or ename == './src/h5_readFlash.hpp':