Back to custom pybedtools.

install.sh

 #!/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 .

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

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