diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 6f04d436877f..751f3c3aebe3 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -5,13 +5,14 @@
 
 python.buildPythonPackage rec {
   pname = "snakemake";
-  version = "5.2.2";
+  version = "5.4.4";
 
   propagatedBuildInputs = with python; [
     appdirs
     ConfigArgParse
     datrie
     docutils
+    GitPython
     jsonschema
     pyyaml
     ratelimiter
@@ -21,7 +22,7 @@ python.buildPythonPackage rec {
 
   src = python.fetchPypi {
     inherit pname version;
-    sha256 = "adffe7e24b4a613a9e8bf0a2a320b3cea236d86afb9132bb0bbbc08b8e35a3a3";
+    sha256 = "157323e0e1be34302edbbf399b2acbe25a4291bceffd47a0469963a970c9375f";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
diff --git a/pkgs/development/python-modules/datrie/default.nix b/pkgs/development/python-modules/datrie/default.nix
index eb654c650778..7cb30937e0db 100644
--- a/pkgs/development/python-modules/datrie/default.nix
+++ b/pkgs/development/python-modules/datrie/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch
 , cython, pytest, pytestrunner, hypothesis }:
 
 buildPythonPackage rec {
@@ -10,6 +10,14 @@ buildPythonPackage rec {
     sha256 = "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs";
   };
 
+  patches = [
+    # fix tests against recent hypothesis
+    (fetchpatch {
+      url = "https://github.com/pytries/datrie/commit/9b24b4c02783cdb703ac3f6c6d7d881db93166e0.diff";
+      sha256 = "1ql7jcf57q3x3fcbddl26y9kmnbnj2dv6ga8mwq94l4a3213j2iy";
+    })
+  ];
+
   nativeBuildInputs = [ cython ];
   buildInputs = [ pytest pytestrunner hypothesis ];