diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix
index eaf0b5932726..a199e41d50aa 100644
--- a/pkgs/applications/science/biology/deeptools/default.nix
+++ b/pkgs/applications/science/biology/deeptools/default.nix
@@ -2,15 +2,17 @@
 with python.pkgs;
 buildPythonApplication rec {
   pname = "deepTools";
-  version = "3.5.1";
+  version = "3.5.4";
 
   src = fetchFromGitHub {
     owner = "deeptools";
     repo = "deepTools";
     rev = version;
-    sha256 = "07v8vb2x4b0mgw0mvcj91vj1fqbcwizwsniysl2cvmv93gad8gbp";
+    sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI=";
   };
 
+  format = "pyproject";
+
   propagatedBuildInputs = [
     numpy
     numpydoc
@@ -21,9 +23,10 @@ buildPythonApplication rec {
     matplotlib
     plotly
     deeptoolsintervals
+    importlib-metadata
   ];
 
-  nativeCheckInputs = [ nose ];
+  nativeCheckInputs = [ pytest ];
 
   meta = with lib; {
     homepage = "https://deeptools.readthedocs.io/en/develop";
@@ -36,7 +39,7 @@ buildPythonApplication rec {
       publication-ready visualizations to identify enrichments and for functional
       annotations of the genome.
     '';
-    license = licenses.gpl3;
+    license = with licenses; [ mit bsd3 ];
     maintainers = with maintainers; [ scalavision ];
   };
 }