diff --git a/install.sh b/install.sh
index f24e57c24edd55505cfe12231ffa689e0b425492..532590a114310d81732b37dffc3fe9256ae999ed 100755
--- a/install.sh
+++ b/install.sh
@@ -1,5 +1,7 @@
 #!/bin/sh
 /usr/bin/env python3 setup.py build_ext
 # .egg-link does not work with PYTHONPATH ?
+# Install custom pybedtools first
+/usr/bin/env python3 -m pip install -r requirements.txt
 /usr/bin/env python3 -m pip install -e .
 /usr/bin/env python3 -m pip install --no-deps --ignore-installed .
diff --git a/requirements.txt b/requirements.txt
index 4f038f05d19585d543817b3121473664bb3d1f37..641ceef347c80f1b82788a8907cf5a10a2f51b9c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,7 @@ networkx
 numpy
 pandas
 pyBigWig
-# pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
-pybedtools
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+# pybedtools
 scipy
 seaborn
diff --git a/setup.py b/setup.py
index caea281408e4bdc4cafc24f2d53bc2da8674894c..512701d4dc3f0c2d08d5672b1dc71579f207dfc3 100644
--- a/setup.py
+++ b/setup.py
@@ -28,8 +28,8 @@ setup(
         "numpy",
         "pandas",
         "pyBigWig",
-        # "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
-        "pybedtools",
+        "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
+        # "pybedtools",
         "scipy",
         "seaborn"],
     # specific versions and index would rather belong to requirements.txt