diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix
index 1a6555e0d634..5a1bb187886b 100644
--- a/pkgs/applications/science/biology/kallisto/default.nix
+++ b/pkgs/applications/science/biology/kallisto/default.nix
@@ -2,19 +2,21 @@
 
 stdenv.mkDerivation rec {
   pname = "kallisto";
-  version = "0.46.1";
+  version = "0.46.2";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "09ldgy70wziw51ma4a3b7vyrphzf2v1cnq1j5r1wwgfmx8fgbh2z";
+    sha256 = "0m0r2820ca3rch99md1zzbgkilmlfkhdkpys2lfnb87qxmf1jnmb";
   };
 
   nativeBuildInputs = [ autoconf cmake ];
 
   buildInputs = [ hdf5 zlib ];
 
+  cmakeFlags = [ "-DUSE_HDF5=ON" ];
+
   # Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160
   enableParallelBuilding = false;