diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c0e82bb0e89c015f4197ff03f30bd14cd150bd7
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,10 @@
+Cython
+libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git
+matplotlib
+networkx
+numpy
+pandas
+pyBigWig
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+scipy
+seaborn
diff --git a/scripts/sam2indexedbam.sh b/scripts/sam2indexedbam.sh
index a530f7db106557594fe779439620cab2f35f6fc1..99d82b7e911294f2428829068664ea9c19209294 100755
--- a/scripts/sam2indexedbam.sh
+++ b/scripts/sam2indexedbam.sh
@@ -31,6 +31,7 @@ function error_exit
 samtools --version
 
 SAM=${1}
+echo "Will sort and index ${SAM}"
 
 case ${SAM} in
     *.sam)
diff --git a/setup.py b/setup.py
index 5449192a5ae64da5dc4c3a0844f96bc0f9c56682..14c4e758a8dd04a08ae145236d6033345ac64921 100644
--- a/setup.py
+++ b/setup.py
@@ -28,7 +28,7 @@ setup(
         "numpy",
         "pandas",
         "pyBigWig",
-        "pybedtools",
+        "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
         "scipy",
         "seaborn"],
     # specific versions and index would rather belong to requirements.txt