diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 695cf7c48c3..0bb5ee866e5 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -12,9 +12,10 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [ zlib python bzip2 lzma ];
-  cc = if stdenv.cc.isClang then "clang++" else "g++";
-  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
-  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
+  cxx = if stdenv.cc.isClang then "clang++" else "g++";
+  cc = if stdenv.cc.isClang then "clang" else "gcc";
+  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
+  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install";
 
   meta = with stdenv.lib; {
     description = "A powerful toolset for genome arithmetic.";