diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000000000000000000000000000000000..8d8a43b494757272d02ffe0e1fbc99291200b510
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "hicstuff"]
+	path = bin/hicstuff_repo
+	url = https://github.com/koszullab/hicstuff.git
diff --git a/bin/hicstuff_repo b/bin/hicstuff_repo
new file mode 160000
index 0000000000000000000000000000000000000000..9f04d34c89586635cb602e3640bfbc045323caec
--- /dev/null
+++ b/bin/hicstuff_repo
@@ -0,0 +1 @@
+Subproject commit 9f04d34c89586635cb602e3640bfbc045323caec