diff --git a/requirements.txt b/requirements.txt
index a9ddf11c58134b82694a36dd0af884b157abd339..ed3fcb7305de295484a7ebb6b89144450d9eb6b6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 cytoolz
-deeptools
+deeptools @ git+https://github.com/blaiseli/deepTools.git@issue-1041
 gffutils
 libhts @ git+https://gitlab.pasteur.fr/bli/libhts.git@c6820e38561007a87359bffe59a4a0cb2cd3f9ec
 libworkflows @ git+https://gitlab.pasteur.fr/bli/libworkflows.git@b29b854ff1db6c87386007808286207b8af11b9d
diff --git a/setup.py b/setup.py
index 3522fc89345a7b9626edf65184f5367ce2d2a075..4e2acc3fb2300ff965dfe56819123498e8825fae 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@ setup(
         "scripts/plot_scatterplot.py"],
     install_requires=[
         "cytoolz",
-        "deeptools",
+        "deeptools @ git+https://github.com/blaiseli/deepTools.git@issue-1041",
         "gffutils",
         "libhts @ git+https://gitlab.pasteur.fr/bli/libhts.git@c6820e38561007a87359bffe59a4a0cb2cd3f9ec",
         "libworkflows @ git+https://gitlab.pasteur.fr/bli/libworkflows.git@b29b854ff1db6c87386007808286207b8af11b9d",