diff --git a/pkgs/development/python-modules/Theano/default.nix b/pkgs/development/python-modules/Theano/default.nix
index e2b31cdda794..793488f0b136 100644
--- a/pkgs/development/python-modules/Theano/default.nix
+++ b/pkgs/development/python-modules/Theano/default.nix
@@ -1,8 +1,8 @@
 { stdenv
+, runCommandCC
 , lib
 , fetchPypi
 , gcc
-, writeScriptBin
 , buildPythonPackage
 , isPyPy
 , pythonOlder
@@ -24,19 +24,24 @@ assert cudaSupport -> nvidia_x11 != null
                    && cudnn != null;
 
 let
-  extraFlags =
-    lib.optionals cudaSupport [ "-I ${cudatoolkit}/include" "-L ${cudatoolkit}/lib" ]
-    ++ lib.optionals cudnnSupport [ "-I ${cudnn}/include" "-L ${cudnn}/lib" ]
-    ++ lib.optionals cudaSupport [ "-I ${libgpuarray}/include" "-L ${libgpuarray}/lib" ];
+  wrapped = command: buildTop: buildInputs:
+    runCommandCC "${command}-wrapped" { inherit buildInputs; } ''
+      type -P '${command}' || { echo '${command}: not found'; exit 1; }
+      cat > "$out" <<EOF
+      #!$(type -P bash)
+      $(declare -xp | sed -e '/^[^=]\+="\('"''${NIX_STORE//\//\\/}"'\|[^\/]\)/!d')
+      declare -x NIX_BUILD_TOP="${buildTop}"
+      $(type -P '${command}') "\$@"
+      EOF
+      chmod +x "$out"
+    '';
 
-  gcc_ = writeScriptBin "g++" ''
-    #!${stdenv.shell}
-    export NIX_CC_WRAPPER_${stdenv.cc.infixSalt}_TARGET_HOST=1
-    export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE ${toString extraFlags}"
-    exec ${gcc}/bin/g++ "$@"
-  '';
+  # Theano spews warnings and disabled flags if the compiler isn't named g++
+  cxx_compiler = wrapped "g++" "\\$HOME/.theano"
+    (    stdenv.lib.optional cudaSupport libgpuarray_
+      ++ stdenv.lib.optional cudnnSupport cudnn );
 
-  libgpuarray_ = libgpuarray.override { inherit cudaSupport; };
+  libgpuarray_ = libgpuarray.override { inherit cudaSupport cudatoolkit; };
 
 in buildPythonPackage rec {
   pname = "Theano";
@@ -50,12 +55,15 @@ in buildPythonPackage rec {
   };
 
   postPatch = ''
-    sed -i 's,g++,${gcc_}/bin/g++,g' theano/configdefaults.py
-  '' + lib.optionalString cudnnSupport ''
-    sed -i \
-      -e "s,ctypes.util.find_library('cudnn'),'${cudnn}/lib/libcudnn.so',g" \
-      -e "s/= _dnn_check_compile()/= (True, None)/g" \
-      theano/gpuarray/dnn.py
+    substituteInPlace theano/configdefaults.py \
+      --replace 'StrParam(param, is_valid=warn_cxx)' 'StrParam('\'''${cxx_compiler}'\''', is_valid=warn_cxx)' \
+      --replace 'rc == 0 and config.cxx != ""' 'config.cxx != ""'
+  '' + stdenv.lib.optionalString cudaSupport ''
+    substituteInPlace theano/configdefaults.py \
+      --replace 'StrParam(get_cuda_root)' 'StrParam('\'''${cudatoolkit}'\''')'
+  '' + stdenv.lib.optionalString cudnnSupport ''
+    substituteInPlace theano/configdefaults.py \
+      --replace 'StrParam(default_dnn_base_path)' 'StrParam('\'''${cudnn}'\''')'
   '';
 
   preCheck = ''