misc pkgs: Basic sed to get fix `pkgconfig` and `autoreconfHook` `buildInputs`

Only acts on one-line dependency lists.

282 files changed, 608 insertions, 293 deletions

diff --git a/pkgs/development/compilers/dale/default.nix b/pkgs/development/compilers/dale/default.nix
index fae1c1d1b40d..8bae6e2363f6 100644
--- a/pkgs/development/compilers/dale/default.nix
+++ b/pkgs/development/compilers/dale/default.nix
@@ -20,7 +20,8 @@ in stdenv.mkDerivation {
     sha256 = "0dc5cjahv7lzlp92hidlh83rwgrpgb6xz2pnba2pm5xrv2pnsskl";
   };
 
-  buildInputs = [ cmake pkgconfig libffi llvm_35 ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake libffi llvm_35 ]
              ++ stdenv.lib.optional doCheck perl;
 
   patches = [ ./link-llvm.patch ];
diff --git a/pkgs/development/compilers/factor-lang/default.nix b/pkgs/development/compilers/factor-lang/default.nix
index 85caa82a155c..87572661635b 100644
--- a/pkgs/development/compilers/factor-lang/default.nix
+++ b/pkgs/development/compilers/factor-lang/default.nix
@@ -21,7 +21,8 @@ stdenv.mkDerivation rec {
     name = "factorimage";
   };
 
-  buildInputs = [ git rlwrap curl pkgconfig perl makeWrapper
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ git rlwrap curl perl makeWrapper
     libX11 pango cairo gtk2 gdk_pixbuf gtkglext
     mesa libXmu libXt libICE libSM ];
 
diff --git a/pkgs/development/compilers/fsharp/default.nix b/pkgs/development/compilers/fsharp/default.nix
index 751d44a38a4c..af33039d341a 100644
--- a/pkgs/development/compilers/fsharp/default.nix
+++ b/pkgs/development/compilers/fsharp/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0mvmvwwpl4zq0yvgzdizww8l9azvlrc82xm32nz1fi1nw8x5qfqk";
   };
 
-  buildInputs = [ mono pkgconfig dotnetbuildhelpers autoconf automake which ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ mono dotnetbuildhelpers autoconf automake which ];
 
   configurePhase = ''
     sed -i '988d' src/FSharpSource.targets
diff --git a/pkgs/development/compilers/rust/cargo.nix b/pkgs/development/compilers/rust/cargo.nix
index ac4102c9a63c..97977ba3ed3a 100644
--- a/pkgs/development/compilers/rust/cargo.nix
+++ b/pkgs/development/compilers/rust/cargo.nix
@@ -18,7 +18,8 @@ rustPlatform.buildRustPackage rec {
 
   passthru.rustc = rustc;
 
-  buildInputs = [ file curl pkgconfig python openssl cmake zlib makeWrapper libgit2 ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ file curl python openssl cmake zlib makeWrapper libgit2 ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ libiconv ];
 
   LIBGIT2_SYS_USE_PKG_CONFIG=1;
diff --git a/pkgs/development/compilers/yosys/default.nix b/pkgs/development/compilers/yosys/default.nix
index ed374ea68229..35172dbd15ba 100644
--- a/pkgs/development/compilers/yosys/default.nix
+++ b/pkgs/development/compilers/yosys/default.nix
@@ -22,7 +22,8 @@ stdenv.mkDerivation rec {
   ];
   sourceRoot = "yosys";
 
-  buildInputs = [ pkgconfig tcl readline libffi python3 bison flex ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ tcl readline libffi python3 bison flex ];
   preBuild = ''
     chmod -R u+w ../yosys-abc
     ln -s ../yosys-abc abc
diff --git a/pkgs/development/coq-modules/dpdgraph/default.nix b/pkgs/development/coq-modules/dpdgraph/default.nix
index 9dbc3a3f2991..65be1f4e0667 100644
--- a/pkgs/development/coq-modules/dpdgraph/default.nix
+++ b/pkgs/development/coq-modules/dpdgraph/default.nix
@@ -21,7 +21,8 @@ stdenv.mkDerivation {
     inherit (param) rev sha256;
   };
 
-  buildInputs = [ autoreconfHook coq ]
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ coq ]
   ++ (with ocamlPackages; [ ocaml findlib ocamlgraph ]);
 
   preInstall = ''
diff --git a/pkgs/development/guile-modules/guile-cairo/default.nix b/pkgs/development/guile-modules/guile-cairo/default.nix
index 6ba1a59d545a..6611c0745061 100644
--- a/pkgs/development/guile-modules/guile-cairo/default.nix
+++ b/pkgs/development/guile-modules/guile-cairo/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1f5nd9n46n6cwfl1byjml02q3y2hgn7nkx98km1czgwarxl7ws3x";
   };
 
-  buildInputs = [ guile pkgconfig cairo expat ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ guile cairo expat ]
     ++ stdenv.lib.optional doCheck guile_lib;
 
   doCheck = true;
diff --git a/pkgs/development/guile-modules/guile-xcb/default.nix b/pkgs/development/guile-modules/guile-xcb/default.nix
index a60a10c5c042..92d17fbe0db2 100644
--- a/pkgs/development/guile-modules/guile-xcb/default.nix
+++ b/pkgs/development/guile-modules/guile-xcb/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation {
     sha256 = "04dvbqdrrs67490gn4gkq9zk8mqy3mkls2818ha4p0ckhh0pm149";
   };
 
-  buildInputs = [ pkgconfig guile texinfo ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ guile texinfo ];
 
   preConfigure = ''
     configureFlags="
diff --git a/pkgs/development/interpreters/erlang/generic-builder.nix b/pkgs/development/interpreters/erlang/generic-builder.nix
index 897f84f94ada..b41fa8a77c4d 100644
--- a/pkgs/development/interpreters/erlang/generic-builder.nix
+++ b/pkgs/development/interpreters/erlang/generic-builder.nix
@@ -49,7 +49,8 @@ in stdenv.mkDerivation ({
 
   nativeBuildInputs = [ autoreconfHook makeWrapper perl ];
 
-  buildInputs = [ gnum4 ncurses openssl autoreconfHook libxslt libxml2 ]
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ gnum4 ncurses openssl libxslt libxml2 ]
     ++ optionals wxSupport wxPackages2
     ++ optionals odbcSupport odbcPackages
     ++ optionals javacSupport javacPackages
diff --git a/pkgs/development/interpreters/falcon/default.nix b/pkgs/development/interpreters/falcon/default.nix
index 4c4a4a0c8947..857a1e5cd8df 100644
--- a/pkgs/development/interpreters/falcon/default.nix
+++ b/pkgs/development/interpreters/falcon/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1x3gdcz1gqhi060ngqi0ghryf69v8bn50yrbzfad8bhblvhzzdlf";
   };
 
-  buildInputs = [ cmake pkgconfig pcre zlib sqlite ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake pcre zlib sqlite ];
 
   meta = with stdenv.lib; {
     description = "Programming language with macros and syntax at once";
diff --git a/pkgs/development/interpreters/gtk-server/default.nix b/pkgs/development/interpreters/gtk-server/default.nix
index 381144c68c2c..ab295dab4443 100644
--- a/pkgs/development/interpreters/gtk-server/default.nix
+++ b/pkgs/development/interpreters/gtk-server/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0z8ng5rhxc7fpsj3d50h25wkgcnxjfy030jm8r9w9m729w2c9hxb";
   };
 
-  buildInputs = [ libffcall gtk2 pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libffcall gtk2 ];
 
   configureOptions = [ "--with-gtk2" ];
 
diff --git a/pkgs/development/interpreters/nix-exec/default.nix b/pkgs/development/interpreters/nix-exec/default.nix
index dea3f6ec633a..7f38f388c354 100644
--- a/pkgs/development/interpreters/nix-exec/default.nix
+++ b/pkgs/development/interpreters/nix-exec/default.nix
@@ -8,7 +8,8 @@ in stdenv.mkDerivation {
     sha256 = "0slpsnzzzdkf5d9za7j4kr15jr4mn1k9klfsxibzy47b2bx1vkar";
   };
 
-  buildInputs = [ pkgconfig nix git ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ nix git ];
 
   NIX_CFLAGS_COMPILE = "-std=c++1y";
 
diff --git a/pkgs/development/interpreters/php/default.nix b/pkgs/development/interpreters/php/default.nix
index ed018a942273..49d48522186f 100644
--- a/pkgs/development/interpreters/php/default.nix
+++ b/pkgs/development/interpreters/php/default.nix
@@ -20,7 +20,8 @@ let
 
       enableParallelBuilding = true;
 
-      buildInputs = [ flex bison pkgconfig ]
+  nativeBuildInputs = [ pkgconfig ];
+      buildInputs = [ flex bison ]
         ++ lib.optional stdenv.isLinux systemd;
 
       flags = {
diff --git a/pkgs/development/interpreters/pixie/default.nix b/pkgs/development/interpreters/pixie/default.nix
index 08ed8f0d4689..9e9a99e52879 100644
--- a/pkgs/development/interpreters/pixie/default.nix
+++ b/pkgs/development/interpreters/pixie/default.nix
@@ -33,7 +33,8 @@ let
     name = "pixie-${version}";
     version = "0-r${commit-count}-${variant}";
     nativeBuildInputs = libs;
-    buildInputs = [ pkgconfig makeWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ makeWrapper ];
     PYTHON = if buildWithPypy
       then "${pypy}/pypy-c/.pypy-c-wrapped"
       else "${python2.interpreter}";
diff --git a/pkgs/development/interpreters/python/pypy/2.7/default.nix b/pkgs/development/interpreters/python/pypy/2.7/default.nix
index 0ea70cc022db..1d382207e989 100644
--- a/pkgs/development/interpreters/python/pypy/2.7/default.nix
+++ b/pkgs/development/interpreters/python/pypy/2.7/default.nix
@@ -37,7 +37,8 @@ in stdenv.mkDerivation rec {
       substituteInPlace "lib-python/2.7/lib-tk/Tix.py" --replace "os.environ.get('TIX_LIBRARY')" "os.environ.get('TIX_LIBRARY') or '${tix}/lib'"
     '';
 
-    buildInputs = [ bzip2 openssl pkgconfig pythonForPypy libffi ncurses expat sqlite tk tcl xlibsWrapper libX11 makeWrapper gdbm db ]
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ bzip2 openssl pythonForPypy libffi ncurses expat sqlite tk tcl xlibsWrapper libX11 makeWrapper gdbm db ]
       ++ stdenv.lib.optional (stdenv ? cc && stdenv.cc.libc != null) stdenv.cc.libc
       ++ stdenv.lib.optional zlibSupport zlib;
 
diff --git a/pkgs/development/interpreters/spidermonkey/1.8.5.nix b/pkgs/development/interpreters/spidermonkey/1.8.5.nix
index ed09ac7467d4..418ee90533f1 100644
--- a/pkgs/development/interpreters/spidermonkey/1.8.5.nix
+++ b/pkgs/development/interpreters/spidermonkey/1.8.5.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
 
   propagatedBuildInputs = [ nspr ];
 
-  buildInputs = [ pkgconfig perl python2 zip ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ perl python2 zip ];
   nativeBuildInputs = if stdenv.isArm then [ autoconf213 ] else [];
 
   postUnpack = "sourceRoot=\${sourceRoot}/js/src";
diff --git a/pkgs/development/interpreters/spidermonkey/17.nix b/pkgs/development/interpreters/spidermonkey/17.nix
index 33acb792f761..da5fc193a222 100644
--- a/pkgs/development/interpreters/spidermonkey/17.nix
+++ b/pkgs/development/interpreters/spidermonkey/17.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
 
   propagatedBuildInputs = [ nspr ];
 
-  buildInputs = [ pkgconfig perl python2 zip libffi readline ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ perl python2 zip libffi readline ];
 
   postUnpack = "sourceRoot=\${sourceRoot}/js/src";
 
diff --git a/pkgs/development/libraries/SDL_sixel/default.nix b/pkgs/development/libraries/SDL_sixel/default.nix
index 5b8e887c2eee..6279bfcb4286 100644
--- a/pkgs/development/libraries/SDL_sixel/default.nix
+++ b/pkgs/development/libraries/SDL_sixel/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
 
   configureFlags = [ "--enable-video-sixel" ];
 
-  buildInputs = [ pkgconfig libsixel ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libsixel ];
 
   meta = with stdenv.lib; {
     description = "A cross-platform multimedia library, that supports sixel graphics on consoles";
diff --git a/pkgs/development/libraries/Xaw3d/default.nix b/pkgs/development/libraries/Xaw3d/default.nix
index 50399f62d0a5..8cadc7290aa9 100644
--- a/pkgs/development/libraries/Xaw3d/default.nix
+++ b/pkgs/development/libraries/Xaw3d/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
       ];
     sha256 = "099kx6ni5vkgr3kf40glif8m6r1m1hq6hxqlqrblaj1w5cphh8hi";
   };
-  buildInputs = [imake gccmakedep libXpm libXp bison flex pkgconfig];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [imake gccmakedep libXpm libXp bison flex];
   propagatedBuildInputs = [xlibsWrapper libXmu];
 
   meta = {
diff --git a/pkgs/development/libraries/afflib/default.nix b/pkgs/development/libraries/afflib/default.nix
index 7c697d3e60c9..b398af0db344 100644
--- a/pkgs/development/libraries/afflib/default.nix
+++ b/pkgs/development/libraries/afflib/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
     sha256 = "0piwkmg7jn64h57cjf5cybyvyqxj2k752g9vrf4ycds7nhvvbnb6";
   };
 
-  buildInputs = [ zlib curl expat fuse openssl autoreconfHook python ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ zlib curl expat fuse openssl python ];
 
   meta = {
     homepage = http://afflib.sourceforge.net/;
diff --git a/pkgs/development/libraries/agg/default.nix b/pkgs/development/libraries/agg/default.nix
index 8b8d3a29193f..2edf4e232260 100644
--- a/pkgs/development/libraries/agg/default.nix
+++ b/pkgs/development/libraries/agg/default.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation rec {
     url = "http://www.antigrain.com/${name}.tar.gz";
     sha256 = "07wii4i824vy9qsvjsgqxppgqmfdxq0xa87i5yk53fijriadq7mb";
   };
-  buildInputs = [ autoconf automake libtool pkgconfig freetype SDL libX11 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool freetype SDL libX11 ];
 
   # fix build with new automake, from Gentoo ebuild
   preConfigure = ''
diff --git a/pkgs/development/libraries/at-spi2-atk/default.nix b/pkgs/development/libraries/at-spi2-atk/default.nix
index 30fe8173e86f..904c079c84d8 100644
--- a/pkgs/development/libraries/at-spi2-atk/default.nix
+++ b/pkgs/development/libraries/at-spi2-atk/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "60dc90ac4f74b8ffe96a9363c25208a443b381bacecfefea6de549f20ed6957d";
   };
 
-  buildInputs = [ python pkgconfig popt atk libX11 libICE xorg.libXtst libXi
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python popt atk libX11 libICE xorg.libXtst libXi
                   intltool dbus_glib at_spi2_core libSM ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/audio/jamomacore/default.nix b/pkgs/development/libraries/audio/jamomacore/default.nix
index 5dac4d8e5925..7057b020d429 100644
--- a/pkgs/development/libraries/audio/jamomacore/default.nix
+++ b/pkgs/development/libraries/audio/jamomacore/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1hb9b6qc18rsvzvixgllknn756m6zwcn22c79rdibbyz1bhrcnln";
   };
 
-  buildInputs = [ pkgconfig alsaLib portaudio portmidi libsndfile cmake libxml2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ alsaLib portaudio portmidi libsndfile cmake libxml2 ];
 
   meta = {
     description = "A C++ platform for building dynamic and reflexive systems with an emphasis on audio and media";
diff --git a/pkgs/development/libraries/audio/libbs2b/default.nix b/pkgs/development/libraries/audio/libbs2b/default.nix
index a21f698fa896..3a4c363e23c8 100644
--- a/pkgs/development/libraries/audio/libbs2b/default.nix
+++ b/pkgs/development/libraries/audio/libbs2b/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0vz442kkjn2h0dlxppzi4m5zx8qfyrivq581n06xzvnyxi5rg6a7";
   };
 
-  buildInputs = [ pkgconfig libsndfile ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libsndfile ];
 
   hardeningDisable = [ "format" ];
 
diff --git a/pkgs/development/libraries/audio/libsmf/default.nix b/pkgs/development/libraries/audio/libsmf/default.nix
index dce2e363cda5..fe0e0854a327 100644
--- a/pkgs/development/libraries/audio/libsmf/default.nix
+++ b/pkgs/development/libraries/audio/libsmf/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1527pcc1vd0l5iks2yw8m0bymcrnih2md5465lwpzw0wgy4rky7n";
   };
 
-  buildInputs = [ autoreconfHook glib pkgconfig ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ glib ];
 
   meta = with stdenv.lib; {
     description = "A C library for reading and writing Standard MIDI Files";
diff --git a/pkgs/development/libraries/audio/lilv/default.nix b/pkgs/development/libraries/audio/lilv/default.nix
index 87ff0bdb0b6e..427625d6fc67 100644
--- a/pkgs/development/libraries/audio/lilv/default.nix
+++ b/pkgs/development/libraries/audio/lilv/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "08m5a372pr1l7aii9s3pic5nm68gynx1n1bc7bnlswziq6qnbv7p";
   };
 
-  buildInputs = [ lv2 pkgconfig python serd sord sratom ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ lv2 python serd sord sratom ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/audio/lv2/default.nix b/pkgs/development/libraries/audio/lv2/default.nix
index dafd39efee98..3df8f5e30789 100644
--- a/pkgs/development/libraries/audio/lv2/default.nix
+++ b/pkgs/development/libraries/audio/lv2/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0chxwys3vnn3nxc9x2vchm74s9sx0vfra6y893byy12ci61jc1dq";
   };
 
-  buildInputs = [ gtk2 libsndfile pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 libsndfile python ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/audio/lv2/unstable.nix b/pkgs/development/libraries/audio/lv2/unstable.nix
index 034282c4f3a5..595dd9e0a536 100644
--- a/pkgs/development/libraries/audio/lv2/unstable.nix
+++ b/pkgs/development/libraries/audio/lv2/unstable.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1sx39j0gary2nayzv7xgqcra7z1rcw9hrafkji05aksdwf7q0pdm";
   };
 
-  buildInputs = [ gtk2 libsndfile pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 libsndfile python ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/audio/raul/default.nix b/pkgs/development/libraries/audio/raul/default.nix
index 94102c385497..b0b0c6bc59af 100644
--- a/pkgs/development/libraries/audio/raul/default.nix
+++ b/pkgs/development/libraries/audio/raul/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1lby508fb0n8ks6iz959sh18fc37br39d6pbapwvbcw5nckdrxwj";
   };
 
-  buildInputs = [ boost gtk2 pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ boost gtk2 python ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/audio/rtmidi/default.nix b/pkgs/development/libraries/audio/rtmidi/default.nix
index b41db495dbae..022c55045967 100644
--- a/pkgs/development/libraries/audio/rtmidi/default.nix
+++ b/pkgs/development/libraries/audio/rtmidi/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "11pl45lp8sq5xkpipwk622w508nw0qcxr03ibicqn1lsws0hva96";
   };
 
-  buildInputs = [ autoconf automake libtool libjack2 alsaLib pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool libjack2 alsaLib ];
 
   preConfigure = ''
     ./autogen.sh --no-configure
diff --git a/pkgs/development/libraries/audio/sratom/default.nix b/pkgs/development/libraries/audio/sratom/default.nix
index 816baa5221e6..d30cb1d369eb 100644
--- a/pkgs/development/libraries/audio/sratom/default.nix
+++ b/pkgs/development/libraries/audio/sratom/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0hrxd9i66s06bpn6i3s9ka95134g3sm8yscmif7qgdzhyjqw42j4";
   };
 
-  buildInputs = [ lv2 pkgconfig python serd sord ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ lv2 python serd sord ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/audio/suil/default.nix b/pkgs/development/libraries/audio/suil/default.nix
index 8864d710174a..b2cfb0be8bec 100644
--- a/pkgs/development/libraries/audio/suil/default.nix
+++ b/pkgs/development/libraries/audio/suil/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     sha256 = "1kji3lhha26qr6xm9j8ic5c40zbrrb5qnwm2qxzmsfxgmrz29wkf";
   };
 
-  buildInputs = [ gtk2 lv2 pkgconfig python serd sord sratom ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 lv2 python serd sord sratom ]
     ++ (lib.optionals withQt4 [ qt4 ])
     ++ (lib.optionals withQt5 (with qt5; [ qtbase qttools ]));
 
diff --git a/pkgs/development/libraries/audio/vamp/default.nix b/pkgs/development/libraries/audio/vamp/default.nix
index f4c4220a8792..8cae07e29490 100644
--- a/pkgs/development/libraries/audio/vamp/default.nix
+++ b/pkgs/development/libraries/audio/vamp/default.nix
@@ -13,7 +13,8 @@ rec {
       sha256 = "178kfgq08cmgdzv7g8dwyjp4adwx8q04riimncq4nqkm8ng9ywbv";
     };
 
-    buildInputs = [ pkgconfig libsndfile ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ libsndfile ];
 
     meta = with stdenv.lib; {
       description = "Audio processing plugin system for plugins that extract descriptive information from audio data";
diff --git a/pkgs/development/libraries/biblesync/default.nix b/pkgs/development/libraries/biblesync/default.nix
index 9cf4bb22e58d..e6702d0db640 100644
--- a/pkgs/development/libraries/biblesync/default.nix
+++ b/pkgs/development/libraries/biblesync/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec{
     sha256 = "0190q2da0ppif2242lahl8xfz01n9sijy60aq1a0545qcp0ilvl8";
   };
 
-  buildInputs = [ pkgconfig cmake libuuid ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake libuuid ];
 
   meta = {
     homepage = http://www.crosswire.org/wiki/BibleSync;
diff --git a/pkgs/development/libraries/blitz/default.nix b/pkgs/development/libraries/blitz/default.nix
index 498c8f005f0f..5ae9ead9ced4 100644
--- a/pkgs/development/libraries/blitz/default.nix
+++ b/pkgs/development/libraries/blitz/default.nix
@@ -31,7 +31,8 @@ stdenv.mkDerivation rec {
 
   patches = [ ./blitz-gcc47.patch ./blitz-testsuite-stencil-et.patch ];
 
-  buildInputs = [ pkgconfig gfortran texinfo ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gfortran texinfo ]
     ++ optional (boost != null) boost;
 
   configureFlags =
diff --git a/pkgs/development/libraries/ccrtp/1.8.nix b/pkgs/development/libraries/ccrtp/1.8.nix
index 0bdffc9d3570..bd83a5c79d55 100644
--- a/pkgs/development/libraries/ccrtp/1.8.nix
+++ b/pkgs/development/libraries/ccrtp/1.8.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
     sha256 = "0wr4dandlfajhmg90nqyvwv61ikn9vdycji001310y3c4zfysprn";
   };
 
-  buildInputs = [ openssl pkgconfig libgcrypt commoncpp2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ openssl libgcrypt commoncpp2 ];
 
   patches = [ ./gcc-4.6-fix.patch ];
 
diff --git a/pkgs/development/libraries/ctl/default.nix b/pkgs/development/libraries/ctl/default.nix
index 4d30afe6818c..a4f49dea59af 100644
--- a/pkgs/development/libraries/ctl/default.nix
+++ b/pkgs/development/libraries/ctl/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
 
   src = source.src;
 
-  buildInputs = [ cmake pkgconfig libtiff ilmbase openexr ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake libtiff ilmbase openexr ];
 
   meta = with stdenv.lib; {
     description = "Color Transformation Language";
diff --git a/pkgs/development/libraries/ctpl/default.nix b/pkgs/development/libraries/ctpl/default.nix
index 6ee04ae57952..fd8fa1a994d6 100644
--- a/pkgs/development/libraries/ctpl/default.nix
+++ b/pkgs/development/libraries/ctpl/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1yr92xv9n6kgyixwg9ps4zb404ic5pgb171k4bi3mv9p6k8gv59s";
   };
 
-  buildInputs = [ pkgconfig glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ];
 
   meta = with stdenv.lib; {
     homepage = http://ctpl.tuxfamily.org/;
diff --git a/pkgs/development/libraries/cwiid/default.nix b/pkgs/development/libraries/cwiid/default.nix
index fb5431ff8d59..fe7c1314feb0 100644
--- a/pkgs/development/libraries/cwiid/default.nix
+++ b/pkgs/development/libraries/cwiid/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     sed -i -e '/$(LDCONFIG)/d' common/include/lib.mak.in
   '';
 
-  buildInputs = [ autoreconfHook bison flex bluez pkgconfig gtk2 ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ bison flex bluez gtk2 ];
 
   postInstall = ''
     # Some programs (for example, cabal-install) have problems with the double 0
diff --git a/pkgs/development/libraries/dbus-cplusplus/default.nix b/pkgs/development/libraries/dbus-cplusplus/default.nix
index 5bf9832843b4..ee7afbbf2522 100644
--- a/pkgs/development/libraries/dbus-cplusplus/default.nix
+++ b/pkgs/development/libraries/dbus-cplusplus/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     sha256 = "0rwcz9pvc13b3yfr0lkifnfz0vb5q6dg240bzgf37ni4s8rpc72g";
   })];
 
-  buildInputs = [ dbus glib pkgconfig expat ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ dbus glib expat ];
 
   configureFlags = "--disable-ecore";
 
diff --git a/pkgs/development/libraries/directfb/default.nix b/pkgs/development/libraries/directfb/default.nix
index b4dd865dec01..7279d5c383c4 100644
--- a/pkgs/development/libraries/directfb/default.nix
+++ b/pkgs/development/libraries/directfb/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation {
 
   nativeBuildInputs = [ perl ];
 
-  buildInputs = [ pkgconfig zlib libjpeg freetype giflib libpng ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zlib libjpeg freetype giflib libpng ]
     ++ stdenv.lib.optional enableSDL SDL
     ++ stdenv.lib.optionals enableX11 (with xorg; [
       xproto libX11 libXext #xextproto
diff --git a/pkgs/development/libraries/dotconf/default.nix b/pkgs/development/libraries/dotconf/default.nix
index 61a85c7cd607..efadff6a1138 100644
--- a/pkgs/development/libraries/dotconf/default.nix
+++ b/pkgs/development/libraries/dotconf/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1sc95hw5k2xagpafny0v35filmcn05k1ds5ghkldfpf6xw4hakp7";
   };
 
-  buildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ];
 
   meta = with stdenv.lib; {
     description = "A configuration parser library";
diff --git a/pkgs/development/libraries/enchant/default.nix b/pkgs/development/libraries/enchant/default.nix
index 02a422c2c843..7363a0239352 100644
--- a/pkgs/development/libraries/enchant/default.nix
+++ b/pkgs/development/libraries/enchant/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g";
   };
   
-  buildInputs = [aspell pkgconfig glib hunspell hspell];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [aspell glib hunspell hspell];
   
   meta = {
     homepage = http://www.abisource.com/enchant;
diff --git a/pkgs/development/libraries/exosip/default.nix b/pkgs/development/libraries/exosip/default.nix
index a5dba0c94f12..bd12dac4aafb 100644
--- a/pkgs/development/libraries/exosip/default.nix
+++ b/pkgs/development/libraries/exosip/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   };
  
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ libosip openssl pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libosip openssl ];
       
   meta = with stdenv.lib; {
     license = licenses.gpl2Plus;
diff --git a/pkgs/development/libraries/fflas-ffpack/1.nix b/pkgs/development/libraries/fflas-ffpack/1.nix
index e5b0592daab3..c723885a68bf 100644
--- a/pkgs/development/libraries/fflas-ffpack/1.nix
+++ b/pkgs/development/libraries/fflas-ffpack/1.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation rec {
     url = "http://linalg.org/fflas-ffpack-${version}.tar.gz";
     sha256 = "02fr675278c65hfiy1chb903j4ix9i8yni1xc2g5nmsjcaf9vra9";
   };
-  buildInputs = [autoreconfHook givaro_3_7 openblas gmpxx];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ givaro_3_7 openblas gmpxx];
   nativeBuildInputs = [pkgconfig];
   configureFlags = "--with-blas=-lopenblas --with-gmp=${gmpxx.dev} --with-givaro=${givaro_3_7}";
   meta = {
diff --git a/pkgs/development/libraries/fflas-ffpack/default.nix b/pkgs/development/libraries/fflas-ffpack/default.nix
index 22f4b6ceef08..f1d6e47f56eb 100644
--- a/pkgs/development/libraries/fflas-ffpack/default.nix
+++ b/pkgs/development/libraries/fflas-ffpack/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     rev = "v${version}";
     sha256 = "0k1f4pb7azrm6ajncvg7vni7ixfmn6fssd5ld4xddbi6jqbsf9rd";
   };
-  buildInputs = [autoreconfHook givaro (liblapack.override {shared = true;}) openblas];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ givaro (liblapack.override {shared = true;}) openblas];
   nativeBuildInputs = [pkgconfig];
   configureFlags = "--with-blas-libs=-lopenblas --with-lapack-libs=-llapack";
   meta = {
diff --git a/pkgs/development/libraries/fontconfig/2.10.nix b/pkgs/development/libraries/fontconfig/2.10.nix
index 7eaba8f75ec4..3f3c04b15a30 100644
--- a/pkgs/development/libraries/fontconfig/2.10.nix
+++ b/pkgs/development/libraries/fontconfig/2.10.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
   outputs = [ "bin" "dev" "lib" "out" ]; # $out contains all the config
 
   propagatedBuildInputs = [ freetype ];
-  buildInputs = [ pkgconfig expat ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ expat ];
 
   configureFlags = [
     "--sysconfdir=/etc"
diff --git a/pkgs/development/libraries/fontconfig/default.nix b/pkgs/development/libraries/fontconfig/default.nix
index f176aa0878c8..9c4116c8f0ba 100644
--- a/pkgs/development/libraries/fontconfig/default.nix
+++ b/pkgs/development/libraries/fontconfig/default.nix
@@ -45,7 +45,8 @@ stdenv.mkDerivation rec {
   outputs = [ "bin" "dev" "lib" "out" ]; # $out contains all the config
 
   propagatedBuildInputs = [ freetype ];
-  buildInputs = [ pkgconfig expat ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ expat ];
 
   configureFlags = [
     "--with-cache-dir=/var/cache/fontconfig" # otherwise the fallback is in $out/
diff --git a/pkgs/development/libraries/frei0r/default.nix b/pkgs/development/libraries/frei0r/default.nix
index 9614762ef2a3..1c0c4c3ace8e 100644
--- a/pkgs/development/libraries/frei0r/default.nix
+++ b/pkgs/development/libraries/frei0r/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0pji26fpd0dqrx1akyhqi6729s394irl73dacnyxk58ijqq4dhp0";
   };
 
-  buildInputs = [ autoconf cairo opencv pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf cairo opencv ];
 
   meta = with stdenv.lib; {
     homepage = http://frei0r.dyne.org;
diff --git a/pkgs/development/libraries/ganv/default.nix b/pkgs/development/libraries/ganv/default.nix
index 7530d82a7e31..5a21af6a2b33 100644
--- a/pkgs/development/libraries/ganv/default.nix
+++ b/pkgs/development/libraries/ganv/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0xmbykdl42jn9cgzrqrys5lng67d26nk5xq10wkkvjqldiwdck56";
   };
 
-  buildInputs = [ graphviz gtk2 gtkmm2 pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ graphviz gtk2 gtkmm2 python ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/gcab/default.nix b/pkgs/development/libraries/gcab/default.nix
index 11308a93337e..38a36fc4e546 100644
--- a/pkgs/development/libraries/gcab/default.nix
+++ b/pkgs/development/libraries/gcab/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1vxdsiky3492zlyrym02sdwf09y19rl2z5h5iin7qm0wizw5wvm1";
   };
 
-  buildInputs = [ intltool gobjectIntrospection pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ intltool gobjectIntrospection ];
 
   meta = with stdenv.lib; {
     platforms = platforms.linux;
diff --git a/pkgs/development/libraries/gdata-sharp/default.nix b/pkgs/development/libraries/gdata-sharp/default.nix
index e9f5898e2eac..40e9b0ed90d5 100644
--- a/pkgs/development/libraries/gdata-sharp/default.nix
+++ b/pkgs/development/libraries/gdata-sharp/default.nix
@@ -12,7 +12,8 @@ in stdenv.mkDerivation rec {
     sha256 = "0b0rvgg3xsbbg2fdrpz0ywsy9rcahlyfskndaagd3yzm83gi6bhk";
   };
 
-  buildInputs = [ pkgconfig mono newtonsoft-json ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ mono newtonsoft-json ];
 
   sourceRoot = "svn-r1217/clients/cs";
 
diff --git a/pkgs/development/libraries/gdome2/default.nix b/pkgs/development/libraries/gdome2/default.nix
index e9643da221ef..306f228051bb 100644
--- a/pkgs/development/libraries/gdome2/default.nix
+++ b/pkgs/development/libraries/gdome2/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation {
 
   hardeningDisable = [ "format" ];
 
-  buildInputs = [pkgconfig glib libxml2 gtkdoc];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib libxml2 gtkdoc];
   propagatedBuildInputs = [glib libxml2];
   patches = [ ./xml-document.patch ];
 
diff --git a/pkgs/development/libraries/geoclue/default.nix b/pkgs/development/libraries/geoclue/default.nix
index 433a1722e76f..f75290005391 100644
--- a/pkgs/development/libraries/geoclue/default.nix
+++ b/pkgs/development/libraries/geoclue/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "15j619kvmdgj2hpma92mkxbzjvgn8147a7500zl3bap9g8bkylqg";
   };
 
-  buildInputs = [ pkgconfig libxml2 gnome2.GConf libxslt glib_networking ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxml2 gnome2.GConf libxslt glib_networking ];
 
   propagatedBuildInputs = [dbus glib dbus_glib];
 
diff --git a/pkgs/development/libraries/givaro/3.7.nix b/pkgs/development/libraries/givaro/3.7.nix
index 9907ae24f2c9..3101bc64333e 100644
--- a/pkgs/development/libraries/givaro/3.7.nix
+++ b/pkgs/development/libraries/givaro/3.7.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation rec {
     url = "https://forge.imag.fr/frs/download.php/370/givaro-${version}.tar.gz";
     sha256 = "0lf5cnbyr27fw7klc3zabkb1979dn67jmrjz6pa3jzw2ng74x9b3";
   };
-  buildInputs = [autoconf automake libtool autoreconfHook gmpxx];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [autoconf automake libtool gmpxx];
   meta = {
     inherit version;
     description = ''A C++ library for arithmetic and algebraic computations'';
diff --git a/pkgs/development/libraries/givaro/3.nix b/pkgs/development/libraries/givaro/3.nix
index bb0fd0e08982..d73a448f1662 100644
--- a/pkgs/development/libraries/givaro/3.nix
+++ b/pkgs/development/libraries/givaro/3.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation rec {
     url = "https://forge.imag.fr/frs/download.php/592/givaro-${version}.tar.gz";
     sha256 = "1822ksv8653a84hvcz0vxl3nk8dqz7d41ys8rplq0zjjmvb2i5yq";
   };
-  buildInputs = [autoconf automake libtool autoreconfHook gmpxx];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [autoconf automake libtool gmpxx];
   meta = {
     inherit version;
     description = ''A C++ library for arithmetic and algebraic computations'';
diff --git a/pkgs/development/libraries/givaro/default.nix b/pkgs/development/libraries/givaro/default.nix
index d9a8624b2ea2..335afa566dbe 100644
--- a/pkgs/development/libraries/givaro/default.nix
+++ b/pkgs/development/libraries/givaro/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     rev = "v${version}";
     sha256 = "04n1lyc823z3l1d7mnmqpc9z1pkn646szjchasbfkn74m7cb0qz7";
   };
-  buildInputs = [autoconf automake libtool autoreconfHook gmpxx];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [autoconf automake libtool gmpxx];
   meta = {
     inherit version;
     description = ''A C++ library for arithmetic and algebraic computations'';
diff --git a/pkgs/development/libraries/globalplatform/default.nix b/pkgs/development/libraries/globalplatform/default.nix
index a7dd47aaeb4f..5b55a09db625 100644
--- a/pkgs/development/libraries/globalplatform/default.nix
+++ b/pkgs/development/libraries/globalplatform/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "191s9005xbc7i90bzjk4rlw15licd6m0rls9fxli8jyymz2021zy";
   };
 
-  buildInputs = [ zlib pkgconfig openssl pcsclite ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zlib openssl pcsclite ];
 
   meta = with stdenv.lib; {
     homepage = https://sourceforge.net/p/globalplatform/wiki/Home/;
diff --git a/pkgs/development/libraries/globalplatform/gppcscconnectionplugin.nix b/pkgs/development/libraries/globalplatform/gppcscconnectionplugin.nix
index f147305220c7..10df82196c2e 100644
--- a/pkgs/development/libraries/globalplatform/gppcscconnectionplugin.nix
+++ b/pkgs/development/libraries/globalplatform/gppcscconnectionplugin.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0d3vcrh9z55rbal0dchmj661pqqrav9c400bx1c46grcl1q022ad";
   };
 
-  buildInputs = [ pkgconfig globalplatform openssl pcsclite ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ globalplatform openssl pcsclite ];
 
   meta = with stdenv.lib; {
     homepage = https://sourceforge.net/p/globalplatform/wiki/Home/;
diff --git a/pkgs/development/libraries/gnet/default.nix b/pkgs/development/libraries/gnet/default.nix
index 6b05bda1b3a7..c9431420194a 100644
--- a/pkgs/development/libraries/gnet/default.nix
+++ b/pkgs/development/libraries/gnet/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "1cy78kglzi235md964ikvm0rg801bx0yk9ya8zavndjnaarzqq87";
   };
 
-  buildInputs = [ pkgconfig autoconf automake glib libtool ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake glib libtool ];
 
   preConfigure = "./autogen.sh";
 
diff --git a/pkgs/development/libraries/gnome-sharp/default.nix b/pkgs/development/libraries/gnome-sharp/default.nix
index f95d0720d830..d80144b3d719 100644
--- a/pkgs/development/libraries/gnome-sharp/default.nix
+++ b/pkgs/development/libraries/gnome-sharp/default.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation {
     sha256 = "0cfvs7hw67fp0wimskqd0gdfx323gv6hi0c5pf59krnmhdrl6z8p";
   };
 
-  buildInputs = [ pkgconfig gtk2 mono gtk-sharp-2_0 ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 mono gtk-sharp-2_0 ]
   ++ (with gnome2; [ libart_lgpl gnome_vfs libgnome libgnomecanvas libgnomeui]);
 
   patches = [ ./Makefile.in.patch ];
diff --git a/pkgs/development/libraries/gobject-introspection/default.nix b/pkgs/development/libraries/gobject-introspection/default.nix
index 4c1f6135b495..b26ae9c9d612 100644
--- a/pkgs/development/libraries/gobject-introspection/default.nix
+++ b/pkgs/development/libraries/gobject-introspection/default.nix
@@ -23,7 +23,8 @@ stdenv.mkDerivation rec {
   outputBin = "dev";
   outputMan = "dev"; # tiny pages
 
-  buildInputs = [ flex bison pkgconfig python setupHook/*move .gir*/ ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ flex bison python setupHook/*move .gir*/ ]
     ++ libintlOrEmpty
     ++ stdenv.lib.optional stdenv.isDarwin cctools;
   propagatedBuildInputs = [ libffi glib ];
diff --git a/pkgs/development/libraries/goocanvas/default.nix b/pkgs/development/libraries/goocanvas/default.nix
index 080b781ca31a..0f9b3f85fcd8 100644
--- a/pkgs/development/libraries/goocanvas/default.nix
+++ b/pkgs/development/libraries/goocanvas/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "07kicpcacbqm3inp7zq32ldp95mxx4kfxpaazd0x5jk7hpw2w1qw";
   };
 
-  buildInputs = [ gtk2 cairo glib pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 cairo glib ];
 
   meta = { 
     description = "Canvas widget for GTK+ based on the the Cairo 2D library";
diff --git a/pkgs/development/libraries/grail/default.nix b/pkgs/development/libraries/grail/default.nix
index c8b1c0bdd9be..a48490ffae57 100644
--- a/pkgs/development/libraries/grail/default.nix
+++ b/pkgs/development/libraries/grail/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1wwx5ibjdz5pyd0f5cd1n91y67r68dymxpm2lgd829041xjizvay";
   };
 
-  buildInputs = [ pkgconfig python3 frame ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python3 frame ]
   ++ stdenv.lib.optionals enableX11 [xorg.libX11 xorg.libXtst xorg.libXext xorg.libXi xorg.libXfixes];
 
   configureFlags = stdenv.lib.optional enableX11 "--with-x11";
diff --git a/pkgs/development/libraries/granite/default.nix b/pkgs/development/libraries/granite/default.nix
index ee453963376f..be869063111c 100644
--- a/pkgs/development/libraries/granite/default.nix
+++ b/pkgs/development/libraries/granite/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1pf4jkz3xyn1sqv70063im80ayb5kdsqwqwx11dc7vgypsl458cm";
   };
   cmakeFlags = "-DINTROSPECTION_GIRDIR=share/gir-1.0/ -DINTROSPECTION_TYPELIBDIR=lib/girepository-1.0";
-  buildInputs = [perl cmake vala pkgconfig gobjectIntrospection glib gtk3 gnome3.libgee gettext];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [perl cmake vala gobjectIntrospection glib gtk3 gnome3.libgee gettext];
   meta = {
     description = "An extension to GTK+ used by elementary OS";
     longDescription = "An extension to GTK+ that provides several useful widgets and classes to ease application development. Designed for elementary OS.";
diff --git a/pkgs/development/libraries/gstreamer/legacy/gnonlin/default.nix b/pkgs/development/libraries/gstreamer/legacy/gnonlin/default.nix
index 608be6538890..402074a4e5f4 100644
--- a/pkgs/development/libraries/gstreamer/legacy/gnonlin/default.nix
+++ b/pkgs/development/libraries/gstreamer/legacy/gnonlin/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0dc9kvr6i7sh91cyhzlbx2bchwg84rfa4679ccppzjf0y65dv8p4";
   };
 
-  buildInputs = [ gst-plugins-base gstreamer pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gst-plugins-base gstreamer ];
 
   meta = {
     homepage = https://gstreamer.freedesktop.org/modules/gnonlin.html;
diff --git a/pkgs/development/libraries/gstreamer/legacy/gstreamer/default.nix b/pkgs/development/libraries/gstreamer/legacy/gstreamer/default.nix
index c20d32e810c4..55d34a3fada3 100644
--- a/pkgs/development/libraries/gstreamer/legacy/gstreamer/default.nix
+++ b/pkgs/development/libraries/gstreamer/legacy/gstreamer/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" ];
 
-  buildInputs = [ perl bison flex pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ perl bison flex ];
   propagatedBuildInputs = [ glib libxml2 ] ++ libintlOrEmpty;
 
   patchPhase = ''
diff --git a/pkgs/development/libraries/gtkimageview/default.nix b/pkgs/development/libraries/gtkimageview/default.nix
index eb0ba2db1030..20584c3850ad 100644
--- a/pkgs/development/libraries/gtkimageview/default.nix
+++ b/pkgs/development/libraries/gtkimageview/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1if3yh5z6nkv5wnkk0qyy9pkk03vn5rqbfk23q87kj39pqscgr37";
   };
 
-  buildInputs = [ pkgconfig gtk2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 ];
 
   preConfigure = ''
     sed '/DEPRECATED_FLAGS/d' -i configure
diff --git a/pkgs/development/libraries/gtkmathview/default.nix b/pkgs/development/libraries/gtkmathview/default.nix
index e36d77142e92..12b9181a952e 100644
--- a/pkgs/development/libraries/gtkmathview/default.nix
+++ b/pkgs/development/libraries/gtkmathview/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
     sha256 = "0hwcamf5fi35frg7q6kgisc9v0prqbhsplb2gl55cg3av9sh3hqx";
   };
 
-  buildInputs = [pkgconfig t1lib glib gmetadom libxml2 popt];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ t1lib glib gmetadom libxml2 popt];
   propagatedBuildInputs = [gtk2 t1lib];
 
   patches = [ ./gcc-4.3-build-fixes.patch ./gcc-4.4-build-fixes.patch ];
diff --git a/pkgs/development/libraries/gtkspell/default.nix b/pkgs/development/libraries/gtkspell/default.nix
index 22b96abf6429..22094f3a3f64 100644
--- a/pkgs/development/libraries/gtkspell/default.nix
+++ b/pkgs/development/libraries/gtkspell/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
     sha256 = "00hdv28bp72kg1mq2jdz1sdw2b8mb9iclsp7jdqwpck705bdriwg";
   };
   
-  buildInputs = [aspell pkgconfig gtk2 enchant intltool];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [aspell gtk2 enchant intltool];
 
   meta = {
     platforms = stdenv.lib.platforms.unix;
diff --git a/pkgs/development/libraries/gts/default.nix b/pkgs/development/libraries/gts/default.nix
index 17ab80ce5868..59b3a34f7bdd 100644
--- a/pkgs/development/libraries/gts/default.nix
+++ b/pkgs/development/libraries/gts/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "07mqx09jxh8cv9753y2d2jsv7wp8vjmrd7zcfpbrddz3wc9kx705";
   };
 
-  buildInputs = [ glib pkgconfig ] ++ stdenv.lib.optional (stdenv.system == "x86_64-darwin") gettext;
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ] ++ stdenv.lib.optional (stdenv.system == "x86_64-darwin") gettext;
 
   meta = {
     homepage = http://gts.sourceforge.net/;
diff --git a/pkgs/development/libraries/hidapi/default.nix b/pkgs/development/libraries/hidapi/default.nix
index 80085759a76a..51c369f7c2d4 100644
--- a/pkgs/development/libraries/hidapi/default.nix
+++ b/pkgs/development/libraries/hidapi/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "13d5jkmh9nh4c2kjch8k8amslnxapa9vkqzrk1z6rqmw8qgvzbkj";
   };
 
-  buildInputs = [ autoreconfHook pkgconfig ]
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ]
     ++ stdenv.lib.optionals stdenv.isLinux [ udev libusb ];
 
   propagatedBuildInputs = stdenv.lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ IOKit Cocoa ]);
diff --git a/pkgs/development/libraries/ignition-transport/generic.nix b/pkgs/development/libraries/ignition-transport/generic.nix
index 5edbf9e4551c..8206338fb080 100644
--- a/pkgs/development/libraries/ignition-transport/generic.nix
+++ b/pkgs/development/libraries/ignition-transport/generic.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
   name = "ign-transport-${version}";
   inherit src;
 
-  buildInputs = [ cmake protobuf zeromq pkgconfig
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake protobuf zeromq
     utillinux # we need utillinux/e2fsprogs uuid/uuid.h
   ];
 
diff --git a/pkgs/development/libraries/ilixi/default.nix b/pkgs/development/libraries/ilixi/default.nix
index 6fd204c236f7..0213148d6930 100644
--- a/pkgs/development/libraries/ilixi/default.nix
+++ b/pkgs/development/libraries/ilixi/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1kmdmqf68jiv7y6as41bhbgdy70yy2i811a3l6kccbazlzpif34v";
   };
 
-  buildInputs = [ pkgconfig directfb libsigcxx libxml2 fontconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ directfb libsigcxx libxml2 fontconfig ];
 
   configureFlags = ''
     --enable-log-debug --enable-debug --enable-trace --with-examples
diff --git a/pkgs/development/libraries/java/classpath/default.nix b/pkgs/development/libraries/java/classpath/default.nix
index 9fb2a2a2e3a1..82e02d06906b 100644
--- a/pkgs/development/libraries/java/classpath/default.nix
+++ b/pkgs/development/libraries/java/classpath/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
 
   patches = [ ./missing-casts.patch ];
 
-  buildInputs = [ javac jvm antlr pkgconfig gtk2 gconf ecj ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ javac jvm antlr gtk2 gconf ecj ];
 
   configurePhase = ''
     # GCJ tries to compile all of Classpath during the `configure' run when
diff --git a/pkgs/development/libraries/java/jzmq/default.nix b/pkgs/development/libraries/java/jzmq/default.nix
index 9a5527b5a131..f86f2fcf2141 100644
--- a/pkgs/development/libraries/java/jzmq/default.nix
+++ b/pkgs/development/libraries/java/jzmq/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ autoreconfHook ];
-  buildInputs = [ pkgconfig zeromq3 jdk ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zeromq3 jdk ];
 
   preConfigure = ''
     ${if stdenv.system == "x86_64-darwin" then
diff --git a/pkgs/development/libraries/languagemachines/frog.nix b/pkgs/development/libraries/languagemachines/frog.nix
index c80c28eb14bc..725bc714db28 100644
--- a/pkgs/development/libraries/languagemachines/frog.nix
+++ b/pkgs/development/libraries/languagemachines/frog.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "frog-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                   libxml2 icu
                   languageMachines.ticcutils
                   languageMachines.timbl
diff --git a/pkgs/development/libraries/languagemachines/frogdata.nix b/pkgs/development/libraries/languagemachines/frogdata.nix
index d9578c380e6d..42d14d083354 100644
--- a/pkgs/development/libraries/languagemachines/frogdata.nix
+++ b/pkgs/development/libraries/languagemachines/frogdata.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "frogdata-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                 ];
 
   preConfigure = ''
diff --git a/pkgs/development/libraries/languagemachines/libfolia.nix b/pkgs/development/libraries/languagemachines/libfolia.nix
index 9cddbdd22d94..d5c232ae7767 100644
--- a/pkgs/development/libraries/languagemachines/libfolia.nix
+++ b/pkgs/development/libraries/languagemachines/libfolia.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "libfolia-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive libxml2 icu languageMachines.ticcutils ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive libxml2 icu languageMachines.ticcutils ];
   preConfigure = "sh bootstrap.sh";
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/languagemachines/mbt.nix b/pkgs/development/libraries/languagemachines/mbt.nix
index 0ba7e686e434..2ffabac1ede9 100644
--- a/pkgs/development/libraries/languagemachines/mbt.nix
+++ b/pkgs/development/libraries/languagemachines/mbt.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "mbt-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                   libxml2
                   languageMachines.ticcutils
                   languageMachines.timbl
diff --git a/pkgs/development/libraries/languagemachines/ticcutils.nix b/pkgs/development/libraries/languagemachines/ticcutils.nix
index f1cb62e68020..738e53556ba6 100644
--- a/pkgs/development/libraries/languagemachines/ticcutils.nix
+++ b/pkgs/development/libraries/languagemachines/ticcutils.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "ticcutils-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive libxml2
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive libxml2
                   # optional:
                   zlib bzip2 libtar
                   # broken but optional: boost
diff --git a/pkgs/development/libraries/languagemachines/timbl.nix b/pkgs/development/libraries/languagemachines/timbl.nix
index 6a60996dc604..d12c970d4dc4 100644
--- a/pkgs/development/libraries/languagemachines/timbl.nix
+++ b/pkgs/development/libraries/languagemachines/timbl.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "timbl-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                   libxml2
                   languageMachines.ticcutils
                 ];
diff --git a/pkgs/development/libraries/languagemachines/timblserver.nix b/pkgs/development/libraries/languagemachines/timblserver.nix
index d8659c9a86b3..7a07e9f33a8a 100644
--- a/pkgs/development/libraries/languagemachines/timblserver.nix
+++ b/pkgs/development/libraries/languagemachines/timblserver.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "timblserver-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                   libxml2
                   languageMachines.ticcutils
                   languageMachines.timbl
diff --git a/pkgs/development/libraries/languagemachines/ucto.nix b/pkgs/development/libraries/languagemachines/ucto.nix
index d60bca412720..5c12a2142cc1 100644
--- a/pkgs/development/libraries/languagemachines/ucto.nix
+++ b/pkgs/development/libraries/languagemachines/ucto.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "ucto-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive
                   icu libxml2
                   languageMachines.ticcutils
                   languageMachines.libfolia
diff --git a/pkgs/development/libraries/languagemachines/uctodata.nix b/pkgs/development/libraries/languagemachines/uctodata.nix
index 33037dbb87fa..56b6448d2533 100644
--- a/pkgs/development/libraries/languagemachines/uctodata.nix
+++ b/pkgs/development/libraries/languagemachines/uctodata.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation {
   version = release.version;
   src = fetchurl { inherit (release) url sha256;
                    name = "uctodata-${release.version}.tar.gz"; };
-  buildInputs = [ automake autoconf libtool pkgconfig autoconf-archive ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool autoconf-archive ];
   preConfigure = "sh bootstrap.sh";
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/lasso/default.nix b/pkgs/development/libraries/lasso/default.nix
index a16a1f431a61..09001b6a6f08 100644
--- a/pkgs/development/libraries/lasso/default.nix
+++ b/pkgs/development/libraries/lasso/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
 
   };
 
-  buildInputs = [ autoconf automake autoreconfHook glib gobjectIntrospection gtk_doc libtool libxml2 libxslt openssl pkgconfig python27Packages.six xmlsec zlib ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ autoconf automake glib gobjectIntrospection gtk_doc libtool libxml2 libxslt openssl python27Packages.six xmlsec zlib ];
 
   configurePhase = ''
     ./configure --with-pkg-config=$PKG_CONFIG_PATH \
diff --git a/pkgs/development/libraries/lensfun/default.nix b/pkgs/development/libraries/lensfun/default.nix
index bd740b757584..5791b0808b4a 100644
--- a/pkgs/development/libraries/lensfun/default.nix
+++ b/pkgs/development/libraries/lensfun/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0cfk8jjhs9nbfjfdy98plrj9ayi59aph0nx6ppslgjhlcvacm2xf";
   };
 
-  buildInputs = [ pkgconfig glib zlib libpng cmake gnumake3 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib zlib libpng cmake gnumake3 ];
 
   configureFlags = "-v";
 
diff --git a/pkgs/development/libraries/libabw/default.nix b/pkgs/development/libraries/libabw/default.nix
index 42abb3d297cb..71a28085541d 100644
--- a/pkgs/development/libraries/libabw/default.nix
+++ b/pkgs/development/libraries/libabw/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
     sed -i 's,^CPPFLAGS.*,\0 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED,' src/lib/Makefile.in
   '';
 
-  buildInputs = [ boost doxygen gperf pkgconfig librevenge libxml2 perl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ boost doxygen gperf librevenge libxml2 perl ];
 
   meta = with stdenv.lib; {
     homepage = https://wiki.documentfoundation.org/DLP/Libraries/libabw;
diff --git a/pkgs/development/libraries/libaudclient/default.nix b/pkgs/development/libraries/libaudclient/default.nix
index 8b3522e2092e..81e32ab2c931 100644
--- a/pkgs/development/libraries/libaudclient/default.nix
+++ b/pkgs/development/libraries/libaudclient/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0nhpgz0kg8r00z54q5i96pjk7s57krq3fvdypq496c7fmlv9kdap";
   };
 
-  buildInputs = [ pkgconfig glib dbus_glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib dbus_glib ];
 
   meta = with stdenv.lib; {
     description = "Legacy D-Bus client library for Audacious";
diff --git a/pkgs/development/libraries/libav/default.nix b/pkgs/development/libraries/libav/default.nix
index 0d075efcd966..1f2349835d53 100644
--- a/pkgs/development/libraries/libav/default.nix
+++ b/pkgs/development/libraries/libav/default.nix
@@ -70,7 +70,8 @@ let
       ++ optional freetypeSupport "--enable-libfreetype"
       ;
 
-    buildInputs = [ pkgconfig lame yasm zlib bzip2 SDL ]
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ lame yasm zlib bzip2 SDL ]
       ++ [ perl ] # for install-man target
       ++ optional mp3Support lame
       ++ optional speexSupport speex
diff --git a/pkgs/development/libraries/libbladeRF/default.nix b/pkgs/development/libraries/libbladeRF/default.nix
index 1411474195d3..8948a74ad630 100644
--- a/pkgs/development/libraries/libbladeRF/default.nix
+++ b/pkgs/development/libraries/libbladeRF/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "1y00hqsmqaix4dql8mb75zx87zvn8b483yxv53x9qyjspksbs60c";
   };
 
-  buildInputs = [ pkgconfig cmake git doxygen help2man tecla libusb1 udev ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake git doxygen help2man tecla libusb1 udev ];
 
   # Fixup shebang
   prePatch = "patchShebangs host/utilities/bladeRF-cli/src/cmd/doc/generate.bash";
diff --git a/pkgs/development/libraries/libcangjie/default.nix b/pkgs/development/libraries/libcangjie/default.nix
index 4692cf6aac12..6838362c7942 100644
--- a/pkgs/development/libraries/libcangjie/default.nix
+++ b/pkgs/development/libraries/libcangjie/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i5svvcx099fc9hh5dvr3gpb1041v6vn5fnylxy82zjy239114lg";
   };
 
-  buildInputs = [ automake autoconf libtool m4 pkgconfig sqlite ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool m4 sqlite ];
 
   configureScript = "./autogen.sh";
   
diff --git a/pkgs/development/libraries/libcdio/0.82.nix b/pkgs/development/libraries/libcdio/0.82.nix
index 632ee9161351..a4b2e6078d2b 100644
--- a/pkgs/development/libraries/libcdio/0.82.nix
+++ b/pkgs/development/libraries/libcdio/0.82.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0fax1dzy84dzs20bmpq2gfw6hc1x2x9mhk53wynhcycjw3l3vjqs";
   };
 
-  buildInputs = [ libcddb pkgconfig ncurses help2man ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libcddb ncurses help2man ]
     ++ stdenv.lib.optional stdenv.isDarwin libiconv;
 
   # Disabled because one test (check_paranoia.sh) fails.
diff --git a/pkgs/development/libraries/libcdio/default.nix b/pkgs/development/libraries/libcdio/default.nix
index 74c95704bbf0..f7596b9c702b 100644
--- a/pkgs/development/libraries/libcdio/default.nix
+++ b/pkgs/development/libraries/libcdio/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1a6x2c5bvpnkn7lhmxkjgz4axmh93m1clrlv41s1wzkc48lnc9zq";
   };
 
-  buildInputs = [ libcddb pkgconfig ncurses help2man ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libcddb ncurses help2man ]
     ++ stdenv.lib.optional stdenv.isDarwin libiconv;
 
   # Disabled because one test (check_paranoia.sh) fails.
diff --git a/pkgs/development/libraries/libcec/default.nix b/pkgs/development/libraries/libcec/default.nix
index 15c40b430401..e60f5e316bd0 100644
--- a/pkgs/development/libraries/libcec/default.nix
+++ b/pkgs/development/libraries/libcec/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation {
     sha256 = "09xsw9hfymzl9fi9r2r8n5cxk80fc00x9drsy1r59pgbycqxvf5q";
   };
 
-  buildInputs = [ cmake pkgconfig udev libcec_platform ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake udev libcec_platform ];
 
   cmakeFlags = [ "-DBUILD_SHARED_LIBS=1" ];
 
diff --git a/pkgs/development/libraries/libchamplain/default.nix b/pkgs/development/libraries/libchamplain/default.nix
index 67302f330b9d..f6d6c5b803eb 100644
--- a/pkgs/development/libraries/libchamplain/default.nix
+++ b/pkgs/development/libraries/libchamplain/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "13snnka1jqc5qrgij8bm22xy02pncf3dn5ij3jh4rrpzq7g1sqpi";
   };
 
-  buildInputs = [ pkgconfig gobjectIntrospection ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gobjectIntrospection ];
 
   propagatedBuildInputs = [ glib gtk3 cairo clutter_gtk sqlite libsoup ];
 
diff --git a/pkgs/development/libraries/libcmis/default.nix b/pkgs/development/libraries/libcmis/default.nix
index 6e0007111bc4..9ab42c7fd1dd 100644
--- a/pkgs/development/libraries/libcmis/default.nix
+++ b/pkgs/development/libraries/libcmis/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
 
   patches = [ ./gcc5.patch ];
 
-  buildInputs = [ boost libxml2 pkgconfig curl autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ boost libxml2 curl ];
   configureFlags = "--without-man --with-boost=${boost.dev} --disable-werror --disable-tests";
 
   # Cppcheck cannot find all the include files (use --check-config for details)
diff --git a/pkgs/development/libraries/libebur128/default.nix b/pkgs/development/libraries/libebur128/default.nix
index e5461d90dd98..8281036e7491 100644
--- a/pkgs/development/libraries/libebur128/default.nix
+++ b/pkgs/development/libraries/libebur128/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "19vy3ldbf931hjvn9jf9dvw1di3yx9ljxyk2yp5cnac1wqiza3jm";
   };
 
-  buildInputs = [ cmake speexdsp pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake speexdsp ];
 
   meta = with stdenv.lib; {
     description = "Implementation of the EBU R128 loudness standard";
diff --git a/pkgs/development/libraries/libee/default.nix b/pkgs/development/libraries/libee/default.nix
index a34ff5edbe2d..7eb5df4c7ecb 100644
--- a/pkgs/development/libraries/libee/default.nix
+++ b/pkgs/development/libraries/libee/default.nix
@@ -7,7 +7,8 @@ stdenv.mkDerivation {
     sha256 = "09xhgzmsq0g3jsyj24vy67bhzk2fv971w5ixdkhfwgar70cw1nn0";
   };
 
-  buildInputs = [pkgconfig libestr];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libestr];
 
   meta = {
     homepage = http://www.libee.org/;
diff --git a/pkgs/development/libraries/libfakekey/default.nix b/pkgs/development/libraries/libfakekey/default.nix
index 4e74762f3f9d..6aca1d2be6d6 100644
--- a/pkgs/development/libraries/libfakekey/default.nix
+++ b/pkgs/development/libraries/libfakekey/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "10msplyn535hmzbmbdnx4zc20hkaw6d81if5lzxs82k8sq2mkx9k";
   };
 
-  buildInputs = [ libX11 libXi libXtst pkgconfig xextproto ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libX11 libXi libXtst xextproto ];
 
   meta = with stdenv.lib; {
     description = "X virtual keyboard library";
diff --git a/pkgs/development/libraries/libfm/default.nix b/pkgs/development/libraries/libfm/default.nix
index d42425c8e185..851ee7f326b6 100644
--- a/pkgs/development/libraries/libfm/default.nix
+++ b/pkgs/development/libraries/libfm/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     sha256 = "0nlvfwh09gbq8bkbvwnw6iqr918rrs9gc9ljb9pjspyg408bn1n7";
   };
 
-  buildInputs = [ glib gtk intltool pango pkgconfig vala_0_34 ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib gtk intltool pango vala_0_34 ]
                 ++ optional (!extraOnly) menu-cache;
 
   configureFlags = [ (optional extraOnly "--with-extra-only")
diff --git a/pkgs/development/libraries/libfreefare/default.nix b/pkgs/development/libraries/libfreefare/default.nix
index 291f20a5db2c..2e8fad3db827 100644
--- a/pkgs/development/libraries/libfreefare/default.nix
+++ b/pkgs/development/libraries/libfreefare/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0r5wfvwgf35lb1v65wavnwz2wlfyfdims6a9xpslf4lsm4a1v8xz";
   };
 
-  buildInputs = [ pkgconfig libnfc openssl ] ++ stdenv.lib.optional stdenv.isDarwin libobjc;
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libnfc openssl ] ++ stdenv.lib.optional stdenv.isDarwin libobjc;
 
   meta = with stdenv.lib; {
     description = "The libfreefare project aims to provide a convenient API for MIFARE card manipulations";
diff --git a/pkgs/development/libraries/libftdi/1.x.nix b/pkgs/development/libraries/libftdi/1.x.nix
index 17cf93473d68..353c82aa1935 100644
--- a/pkgs/development/libraries/libftdi/1.x.nix
+++ b/pkgs/development/libraries/libftdi/1.x.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     sha256 = "1x41mbzh4qy7mrv2n86r2cr176rx03iacn0a99c3dkzv9g4rb34s";
   };
 
-  buildInputs = with stdenv.lib; [ cmake pkgconfig confuse ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = with stdenv.lib; [ cmake confuse ]
     ++ optionals cppSupport [ boost ]
     ++ optionals pythonSupport [ python swig ]
     ++ optionals docSupport [ doxygen ];
diff --git a/pkgs/development/libraries/libgig/default.nix b/pkgs/development/libraries/libgig/default.nix
index fd6e4a7aa482..4adb7e535789 100644
--- a/pkgs/development/libraries/libgig/default.nix
+++ b/pkgs/development/libraries/libgig/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i7sj3zm6banl5avjdxblx0mlbxxzbsbr4x5hsl2fhrdsv5dnxhc";
   };
 
-  buildInputs = [ autoconf automake libsndfile libtool pkgconfig libuuid ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libsndfile libtool libuuid ];
 
   preConfigure = "make -f Makefile.cvs";
 
diff --git a/pkgs/development/libraries/libgringotts/default.nix b/pkgs/development/libraries/libgringotts/default.nix
index 93ad88f0021a..1da6cffe3f2c 100644
--- a/pkgs/development/libraries/libgringotts/default.nix
+++ b/pkgs/development/libraries/libgringotts/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1bzfnpf2gwc2bisbrw06s63g9z9v4mh1n9ksqr6pbgj2prz7bvlk";
   };
 
-  buildInputs = [ pkgconfig zlib bzip2 libmcrypt libmhash ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zlib bzip2 libmcrypt libmhash ];
 
   meta = with stdenv.lib; {
     description = "A small library to encapsulate data in an encrypted structure";
diff --git a/pkgs/development/libraries/libgudev/default.nix b/pkgs/development/libraries/libgudev/default.nix
index 5b29c23fa6e5..ef2a44bf183a 100644
--- a/pkgs/development/libraries/libgudev/default.nix
+++ b/pkgs/development/libraries/libgudev/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "15iz0qp57qy5pjrblsn36l0chlncqggqsg8h8i8c71499afzj7iv";
   };
 
-  buildInputs = [ pkgconfig udev glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ udev glib ];
 
   # There's a dependency cycle with umockdev and the tests fail to LD_PRELOAD anyway.
   configureFlags = [ "--disable-umockdev" ];
diff --git a/pkgs/development/libraries/libinfinity/default.nix b/pkgs/development/libraries/libinfinity/default.nix
index b55e0104f706..835c7d6f2262 100644
--- a/pkgs/development/libraries/libinfinity/default.nix
+++ b/pkgs/development/libraries/libinfinity/default.nix
@@ -18,7 +18,8 @@ in stdenv.mkDerivation rec {
     sha256 = "1idsxb6rz4i55g3vi2sv7hmm57psbccpb57yc4jgphaq6ydgqsr6";
   };
 
-  buildInputs = [ pkgconfig glib libxml2 gsasl libidn gss libintlOrEmpty ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib libxml2 gsasl libidn gss libintlOrEmpty ]
     ++ optional gtkWidgets gtk2
     ++ optional documentation gtkdoc
     ++ optional avahiSupport avahi
diff --git a/pkgs/development/libraries/libiodbc/default.nix b/pkgs/development/libraries/libiodbc/default.nix
index 6f833ec81a92..267d3097c997 100644
--- a/pkgs/development/libraries/libiodbc/default.nix
+++ b/pkgs/development/libraries/libiodbc/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "16hjb6fcval85gnkgkxfhw4c5h3pgf86awyh8p2bhnnvzc0ma5hq";
   };
 
-  buildInputs = stdenv.lib.optionals useGTK [ gtk2 pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = stdenv.lib.optionals useGTK [ gtk2 ];
 
   preBuild =
     ''
diff --git a/pkgs/development/libraries/libjreen/default.nix b/pkgs/development/libraries/libjreen/default.nix
index d539c61a4c95..2167b4477034 100644
--- a/pkgs/development/libraries/libjreen/default.nix
+++ b/pkgs/development/libraries/libjreen/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "14nwwk40xx8w6x7yaysgcr0lgzhs7l064f7ikp32s5y9a8mmp582";
   };
 
-  buildInputs = [ cmake qt4 pkgconfig gsasl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake qt4 gsasl ];
   enableParallelBuilding = true;
 
   meta = {
diff --git a/pkgs/development/libraries/liblogging/default.nix b/pkgs/development/libraries/liblogging/default.nix
index aa75acb7d6d3..4667a6e76014 100644
--- a/pkgs/development/libraries/liblogging/default.nix
+++ b/pkgs/development/libraries/liblogging/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "02w94j344q0ywlj4mdf9fnzwggdsn3j1yn43sdlsddvr29lw239i";
   };
 
-  buildInputs = [ pkgconfig systemd ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ systemd ];
 
   configureFlags = [
     "--enable-rfc3195"
diff --git a/pkgs/development/libraries/liblscp/default.nix b/pkgs/development/libraries/liblscp/default.nix
index a1cbf9250c49..c89b21de0d64 100644
--- a/pkgs/development/libraries/liblscp/default.nix
+++ b/pkgs/development/libraries/liblscp/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0jgdy9gi9n8x2pqrbll9158vhx8293lnxv8vzl0szcincslgk7hi";
   };
 
-  buildInputs = [ autoconf automake libtool pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool ];
 
   preConfigure = "make -f Makefile.svn";
 
diff --git a/pkgs/development/libraries/libmbim/default.nix b/pkgs/development/libraries/libmbim/default.nix
index f1625e6a33fb..b7b05870702b 100644
--- a/pkgs/development/libraries/libmbim/default.nix
+++ b/pkgs/development/libraries/libmbim/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
-  buildInputs = [ pkgconfig glib udev libgudev python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib udev libgudev python ];
 
   meta = with stdenv.lib; {
     homepage = http://www.freedesktop.org/software/libmbim/;
diff --git a/pkgs/development/libraries/libmcs/default.nix b/pkgs/development/libraries/libmcs/default.nix
index 23f333562dc5..a457adfed80f 100644
--- a/pkgs/development/libraries/libmcs/default.nix
+++ b/pkgs/development/libraries/libmcs/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1knmgxrg2kxdlin8qyf6351943ldg8myllwf860af58x1wncxc74";
   };
 
-  buildInputs = [ pkgconfig libmowgli ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libmowgli ];
   
   meta = {
     description = "A library and set of userland tools which abstract the storage of configuration settings away from userland applications";
diff --git a/pkgs/development/libraries/libmesode/default.nix b/pkgs/development/libraries/libmesode/default.nix
index 9dae423efd78..1becd0ee8ef6 100644
--- a/pkgs/development/libraries/libmesode/default.nix
+++ b/pkgs/development/libraries/libmesode/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1zb1x422zkpnxrz9d2b7pmi8ms60lbw49yh78mydqfypsmj2iyfh";
   };
 
-  buildInputs = [ autoreconfHook openssl expat libtool pkgconfig check ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ openssl expat libtool check ];
 
   dontDisableStatic = true;
 
diff --git a/pkgs/development/libraries/libmicrohttpd/default.nix b/pkgs/development/libraries/libmicrohttpd/default.nix
index 23e6a37f918c..b663d22f6447 100644
--- a/pkgs/development/libraries/libmicrohttpd/default.nix
+++ b/pkgs/development/libraries/libmicrohttpd/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
   };
 
   outputs = [ "out" "dev" "devdoc" "info" ];
-  buildInputs = [ libgcrypt curl gnutls pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libgcrypt curl gnutls ];
 
   preCheck = ''
     # Since `localhost' can't be resolved in a chroot, work around it.
diff --git a/pkgs/development/libraries/libmongo-client/default.nix b/pkgs/development/libraries/libmongo-client/default.nix
index 4cbc51ea6786..343622e8d5c7 100644
--- a/pkgs/development/libraries/libmongo-client/default.nix
+++ b/pkgs/development/libraries/libmongo-client/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1cjx06i3gd9zkyvwm2ysjrf0hkhr7bjg3c27s7n0y31j10igfjp0";
   };
 
-  buildInputs = [ autoreconfHook pkgconfig ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ];
   propagatedBuildInputs = [ glib ];
 
   postPatch = ''
diff --git a/pkgs/development/libraries/libmusicbrainz/5.x.nix b/pkgs/development/libraries/libmusicbrainz/5.x.nix
index 4765e90c6df7..f197d5bcef98 100644
--- a/pkgs/development/libraries/libmusicbrainz/5.x.nix
+++ b/pkgs/development/libraries/libmusicbrainz/5.x.nix
@@ -4,7 +4,8 @@ stdenv.mkDerivation rec {
   version = "5.1.0";
   name = "libmusicbrainz-${version}";
 
-  buildInputs = [ cmake neon libdiscid libxml2 pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake neon libdiscid libxml2 ];
 
   src = fetchFromGitHub {
     owner  = "metabrainz";
diff --git a/pkgs/development/libraries/libnetfilter_cthelper/default.nix b/pkgs/development/libraries/libnetfilter_cthelper/default.nix
index 973198409758..fa94fa549e42 100644
--- a/pkgs/development/libraries/libnetfilter_cthelper/default.nix
+++ b/pkgs/development/libraries/libnetfilter_cthelper/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "07618e71c4d9a6b6b3dc1986540486ee310a9838ba754926c7d14a17d8fccf3d";
   };
 
-  buildInputs = [ pkgconfig libmnl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libmnl ];
 
   meta = {
     description = "Userspace library that provides the programming interface to the user-space connection tracking helper infrastructure";
diff --git a/pkgs/development/libraries/libnetfilter_cttimeout/default.nix b/pkgs/development/libraries/libnetfilter_cttimeout/default.nix
index 2920cbd97858..f30e12a41631 100644
--- a/pkgs/development/libraries/libnetfilter_cttimeout/default.nix
+++ b/pkgs/development/libraries/libnetfilter_cttimeout/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "aeab12754f557cba3ce2950a2029963d817490df7edb49880008b34d7ff8feba";
   };
 
-  buildInputs = [ pkgconfig libmnl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libmnl ];
 
   meta = {
     description = "Userspace library that provides the programming interface to the connection tracking timeout infrastructure";
diff --git a/pkgs/development/libraries/libnetfilter_queue/default.nix b/pkgs/development/libraries/libnetfilter_queue/default.nix
index fa4a0f11ef4c..5de9409b729f 100644
--- a/pkgs/development/libraries/libnetfilter_queue/default.nix
+++ b/pkgs/development/libraries/libnetfilter_queue/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0chsmj9ky80068vn458ijz9sh4sk5yc08dw2d6b8yddybpmr1143";
   };
 
-  buildInputs = [ pkgconfig libmnl libnfnetlink ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libmnl libnfnetlink ];
 
   meta = {
     homepage = http://www.netfilter.org/projects/libnetfilter_queue/;
diff --git a/pkgs/development/libraries/libnih/default.nix b/pkgs/development/libraries/libnih/default.nix
index fdbc2ac88003..4903d54b4a31 100644
--- a/pkgs/development/libraries/libnih/default.nix
+++ b/pkgs/development/libraries/libnih/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "01glc6y7z1g726zwpvp2zm79pyb37ki729jkh45akh35fpgp4xc9";
   };
 
-  buildInputs = [ pkgconfig dbus expat ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ dbus expat ];
 
   meta = {
     description = "A small library for C application development";
diff --git a/pkgs/development/libraries/libofx/default.nix b/pkgs/development/libraries/libofx/default.nix
index 7927dba89838..77c049949564 100644
--- a/pkgs/development/libraries/libofx/default.nix
+++ b/pkgs/development/libraries/libofx/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
   };
 
   configureFlags = [ "--with-opensp-includes=${opensp}/include/OpenSP" ];
-  buildInputs = [ opensp pkgconfig libxml2 curl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ opensp libxml2 curl ];
 
   meta = { 
     description = "Opensource implementation of the Open Financial eXchange specification";
diff --git a/pkgs/development/libraries/libotr/default.nix b/pkgs/development/libraries/libotr/default.nix
index ba7a0af0bf54..9be217a800d3 100644
--- a/pkgs/development/libraries/libotr/default.nix
+++ b/pkgs/development/libraries/libotr/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1x8rliydhbibmzwdbyr7pd7n87m2jmxnqkpvaalnf4154hj1hfwb";
   };
 
-  buildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ];
   propagatedBuildInputs = [ libgcrypt ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/libpar2/default.nix b/pkgs/development/libraries/libpar2/default.nix
index 1c88167078f9..6d7606428f69 100644
--- a/pkgs/development/libraries/libpar2/default.nix
+++ b/pkgs/development/libraries/libpar2/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1m4ncws1h03zq7zyqbaymvjzzbh1d3lc4wb1aksrdf0ync76yv9i";
   };
 
-  buildInputs = [ pkgconfig libsigcxx ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libsigcxx ];
 
   patches = [ ./libpar2-0.4-external-verification.patch ];
 
diff --git a/pkgs/development/libraries/libpseudo/default.nix b/pkgs/development/libraries/libpseudo/default.nix
index 34e9bb12754d..c04c8d724d0b 100644
--- a/pkgs/development/libraries/libpseudo/default.nix
+++ b/pkgs/development/libraries/libpseudo/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     mkdir -p $out/lib
   '';
 
-  buildInputs = [ pkgconfig glib ncurses ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ncurses ];
 
   meta = with stdenv.lib; {
     homepage = http://libpseudo.sourceforge.net/;
diff --git a/pkgs/development/libraries/libpst/default.nix b/pkgs/development/libraries/libpst/default.nix
index 9eb3d345ecb7..b19008449abe 100644
--- a/pkgs/development/libraries/libpst/default.nix
+++ b/pkgs/development/libraries/libpst/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
       sha256 = "1m378vxh1sf9ry8k11x773xpy5f6cab5gkzqglz0jp9hc431r60r";
     };
 
-  buildInputs = [ autoreconfHook boost python2 libgsf pkgconfig bzip2
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ boost python2 libgsf bzip2
     xmlto gettext imagemagick doxygen
   ];
 
diff --git a/pkgs/development/libraries/libqmi/default.nix b/pkgs/development/libraries/libqmi/default.nix
index 2e316a30a018..afa8a0451ac0 100644
--- a/pkgs/development/libraries/libqmi/default.nix
+++ b/pkgs/development/libraries/libqmi/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
-  buildInputs = [ pkgconfig glib python libgudev libmbim ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib python libgudev libmbim ];
 
   configureFlags = ["--enable-mbim-qmux" ];
 
diff --git a/pkgs/development/libraries/libqrencode/default.nix b/pkgs/development/libraries/libqrencode/default.nix
index a5e4c4410c09..337d9423aa3d 100644
--- a/pkgs/development/libraries/libqrencode/default.nix
+++ b/pkgs/development/libraries/libqrencode/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0wiagx7i8p9zal53smf5abrnh9lr31mv0p36wg017401jrmf5577";
   };
 
-  buildInputs = [ autoconf automake pkgconfig libtool SDL2 libpng ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool SDL2 libpng ];
 
   propagatedBuildInputs = [ SDL2 libpng ];
 
diff --git a/pkgs/development/libraries/librdf/default.nix b/pkgs/development/libraries/librdf/default.nix
index 945e11d1bcef..8f8a54337f24 100644
--- a/pkgs/development/libraries/librdf/default.nix
+++ b/pkgs/development/libraries/librdf/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
   preAutoreconf = "rm m4/*";
   postPatch = "sed -i -e 's:usr/local:usr:' examples/{instances,remove}_test.c";
 
-  buildInputs = [ pkgconfig autoreconfHook ladspaH openssl zlib ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ladspaH openssl zlib ];
 
   propagatedBuildInputs = [ librdf_raptor2 ];
 
diff --git a/pkgs/development/libraries/librelp/default.nix b/pkgs/development/libraries/librelp/default.nix
index dce85331c1be..adc00b56a287 100644
--- a/pkgs/development/libraries/librelp/default.nix
+++ b/pkgs/development/libraries/librelp/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1mvvxqfsfg96rb6xv3fw7mcsqmyfnsb74sc53gnhpcpp4h2p6m83";
   };
 
-  buildInputs = [ pkgconfig gnutls zlib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gnutls zlib ];
 
   meta = with stdenv.lib; {
     homepage = http://www.librelp.com/;
diff --git a/pkgs/development/libraries/librep/default.nix b/pkgs/development/libraries/librep/default.nix
index cb61982da091..c74a7981458d 100644
--- a/pkgs/development/libraries/librep/default.nix
+++ b/pkgs/development/libraries/librep/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
     sha256 = "1k6c0hmyzxh8459r790slh9vv9vwy9d7w3nlmrqypbx9mk855hgy";
   };
 
-  buildInputs = [ pkgconfig autoreconfHook readline texinfo ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ readline texinfo ];
   propagatedBuildInputs = [ gdbm gmp libffi ];
 
   configureFlags = [
diff --git a/pkgs/development/libraries/librevisa/default.nix b/pkgs/development/libraries/librevisa/default.nix
index 756a53d5ee55..bc39a077e0c4 100644
--- a/pkgs/development/libraries/librevisa/default.nix
+++ b/pkgs/development/libraries/librevisa/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0bjzq23s3xzw0l9qx4l8achrx5id8xdd6r52lvdl4a28dxzbcfhq";
   };
 
-  buildInputs = [ pkgconfig libusb1 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libusb1 ];
 
   meta = with stdenv.lib; {
     description = "Implementation of the VISA standard (for instrument control)";
diff --git a/pkgs/development/libraries/libsearpc/default.nix b/pkgs/development/libraries/libsearpc/default.nix
index 0457c0eb9c49..3898071c8582 100644
--- a/pkgs/development/libraries/libsearpc/default.nix
+++ b/pkgs/development/libraries/libsearpc/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec
 
   patches = [ ./libsearpc.pc.patch ];
 
-  buildInputs = [ automake autoconf pkgconfig libtool python2Packages.python python2Packages.simplejson ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf libtool python2Packages.python python2Packages.simplejson ];
   propagatedBuildInputs = [ glib jansson ];
 
   preConfigure = "./autogen.sh";
diff --git a/pkgs/development/libraries/libserialport/default.nix b/pkgs/development/libraries/libserialport/default.nix
index ab10e34e2301..812847ea123b 100644
--- a/pkgs/development/libraries/libserialport/default.nix
+++ b/pkgs/development/libraries/libserialport/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "17ajlwgvyyrap8z7f16zcs59pksvncwbmd3mzf98wj7zqgczjaja";
   };
 
-  buildInputs = [ pkgconfig udev ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ udev ];
 
   meta = with stdenv.lib; {
     description = "Cross-platform shared library for serial port access";
diff --git a/pkgs/development/libraries/libsigcxx/1.2.nix b/pkgs/development/libraries/libsigcxx/1.2.nix
index 842471a263d9..9fc6ff86773b 100644
--- a/pkgs/development/libraries/libsigcxx/1.2.nix
+++ b/pkgs/development/libraries/libsigcxx/1.2.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "099224v5y0y1ggqrfc8vga8afr3nb93iicn7cj8xxgsrwa83s5nr";
   };
 
-  buildInputs = [pkgconfig m4];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ m4];
 
   meta = {
     homepage = http://libsigc.sourceforge.net/;
diff --git a/pkgs/development/libraries/libsndfile/default.nix b/pkgs/development/libraries/libsndfile/default.nix
index 21710375ed74..53d927219e21 100644
--- a/pkgs/development/libraries/libsndfile/default.nix
+++ b/pkgs/development/libraries/libsndfile/default.nix
@@ -33,7 +33,8 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  buildInputs = [ pkgconfig flac libogg libvorbis ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ flac libogg libvorbis ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ Carbon AudioToolbox ];
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/libspatialite/default.nix b/pkgs/development/libraries/libspatialite/default.nix
index d5e72cae5fce..19ccc9159a3e 100644
--- a/pkgs/development/libraries/libspatialite/default.nix
+++ b/pkgs/development/libraries/libspatialite/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0b9ipmp09y2ij7yajyjsh0zcwps8n5g88lzfzlkph33lail8l4wz";
   };
 
-  buildInputs = [ pkgconfig libxml2 sqlite zlib proj geos libiconv ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxml2 sqlite zlib proj geos libiconv ];
 
   configureFlags = "--disable-freexl";
 
diff --git a/pkgs/development/libraries/libspotify/default.nix b/pkgs/development/libraries/libspotify/default.nix
index 951a939cbfbf..3a01ff2944db 100644
--- a/pkgs/development/libraries/libspotify/default.nix
+++ b/pkgs/development/libraries/libspotify/default.nix
@@ -63,7 +63,8 @@ else stdenv.mkDerivation {
       '' else stdenv.mkDerivation {
         name = "libspotify-samples-${version}";
         src = libspotify.src;
-        buildInputs = [ pkgconfig libspotify readline ]
+  nativeBuildInputs = [ pkgconfig ];
+        buildInputs = [ libspotify readline ]
           ++ stdenv.lib.optional (!stdenv.isDarwin) alsaLib;
         postUnpack = "sourceRoot=$sourceRoot/share/doc/libspotify/examples";
         patchPhase = "cp ${apiKey} appkey.c";
diff --git a/pkgs/development/libraries/libstrophe/default.nix b/pkgs/development/libraries/libstrophe/default.nix
index 76aa014392b0..0d014cb22a82 100644
--- a/pkgs/development/libraries/libstrophe/default.nix
+++ b/pkgs/development/libraries/libstrophe/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "099iv13c03y1dsn2ngdhfx2cnax0aj2gfh00w55hlzpvmjm8dsml";
   };
 
-  buildInputs = [ automake autoconf openssl expat libtool pkgconfig check ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ automake autoconf openssl expat libtool check ];
 
   dontDisableStatic = true;
 
diff --git a/pkgs/development/libraries/libtar/default.nix b/pkgs/development/libraries/libtar/default.nix
index 212a3a23939b..992bad020ea6 100644
--- a/pkgs/development/libraries/libtar/default.nix
+++ b/pkgs/development/libraries/libtar/default.nix
@@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
       (fp "th_get_size-unsigned-int"  "1ravbs5yrfac98mnkrzciw9hd2fxq4dc07xl3wx8y2pv1bzkwm41")
     ];
 
-  buildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ];
 
   meta = with stdenv.lib; {
     description = "C library for manipulating POSIX tar files";
diff --git a/pkgs/development/libraries/libtermkey/default.nix b/pkgs/development/libraries/libtermkey/default.nix
index 97bc98b22d88..429cc5d9f180 100644
--- a/pkgs/development/libraries/libtermkey/default.nix
+++ b/pkgs/development/libraries/libtermkey/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
   makeFlags = [ "PREFIX=$(out)" ]
     ++ stdenv.lib.optional stdenv.isDarwin "LIBTOOL=${libtool}/bin/libtool";
 
-  buildInputs = [ libtool pkgconfig ncurses ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libtool ncurses ];
 
   meta = with lib; {
     description = "Terminal keypress reading library";
diff --git a/pkgs/development/libraries/libtiger/default.nix b/pkgs/development/libraries/libtiger/default.nix
index deab30430359..3a67e1267e20 100644
--- a/pkgs/development/libraries/libtiger/default.nix
+++ b/pkgs/development/libraries/libtiger/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0rj1bmr9kngrgbxrjbn4f4f9pww0wmf6viflinq7ava7zdav4hkk";
   };
 
-  buildInputs = [ libkate pango cairo pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libkate pango cairo ];
 
   meta = {
     homepage = http://code.google.com/p/libtiger/;
diff --git a/pkgs/development/libraries/libtorrent-rasterbar/generic.nix b/pkgs/development/libraries/libtorrent-rasterbar/generic.nix
index d0b69e0348fc..4e1f0badd7a3 100644
--- a/pkgs/development/libraries/libtorrent-rasterbar/generic.nix
+++ b/pkgs/development/libraries/libtorrent-rasterbar/generic.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [automake autoconf libtool ];
 
-  buildInputs = [ boost pkgconfig openssl zlib python libiconv geoip ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ boost openssl zlib python libiconv geoip ];
 
   preConfigure = "./autotool.sh";
 
diff --git a/pkgs/development/libraries/libtsm/default.nix b/pkgs/development/libraries/libtsm/default.nix
index bac29bc0ca8d..58b052b8fae8 100644
--- a/pkgs/development/libraries/libtsm/default.nix
+++ b/pkgs/development/libraries/libtsm/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "01ygwrsxfii0pngfikgqsb4fxp8n1bbs47l7hck81h9b9bc1ah8i";
   };
 
-  buildInputs = [ libxkbcommon pkgconfig ] ++ lib.optionals stdenv.isDarwin [
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxkbcommon ] ++ lib.optionals stdenv.isDarwin [
     autoreconfHook
   ];
 
diff --git a/pkgs/development/libraries/libtxc_dxtn/default.nix b/pkgs/development/libraries/libtxc_dxtn/default.nix
index 170af8f172eb..82aba6b89f5a 100644
--- a/pkgs/development/libraries/libtxc_dxtn/default.nix
+++ b/pkgs/development/libraries/libtxc_dxtn/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0q5fjaknl7s0z206dd8nzk9bdh8g4p23bz7784zrllnarl90saa5";
   };
 
-  buildInputs = [ autoreconfHook mesa ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ mesa ];
 
   meta = {
     homepage = http://dri.freedesktop.org/wiki/S3TC;
diff --git a/pkgs/development/libraries/libtxc_dxtn_s2tc/default.nix b/pkgs/development/libraries/libtxc_dxtn_s2tc/default.nix
index 654bdd2e61f9..387dbb22a816 100644
--- a/pkgs/development/libraries/libtxc_dxtn_s2tc/default.nix
+++ b/pkgs/development/libraries/libtxc_dxtn_s2tc/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0ibfdib277fhbqvxzan0bmglwnsl1y1rw2g8skvz82l1sfmmn752";
   };
 
-  buildInputs = [ autoreconfHook mesa ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ mesa ];
 
   meta = {
     description = "A patent-free S3TC compatible implementation";
diff --git a/pkgs/development/libraries/libui/default.nix b/pkgs/development/libraries/libui/default.nix
index 4db641868508..2f8963db0cd8 100644
--- a/pkgs/development/libraries/libui/default.nix
+++ b/pkgs/development/libraries/libui/default.nix
@@ -13,7 +13,8 @@ in
       sha256 = "1lpbfa298c61aarlzgp7vghrmxg1274pzxh1j9isv8x758gk6mfn";
     };
 
-    buildInputs = [ cmake pkgconfig ] ++
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ cmake ] ++
       (if stdenv.isDarwin then [darwin.apple_sdk.frameworks.Cocoa] else [gtk3]);
 
     preConfigure = stdenv.lib.optionalString stdenv.isDarwin ''
diff --git a/pkgs/development/libraries/libunique/3.x.nix b/pkgs/development/libraries/libunique/3.x.nix
index 8d1077ee6a00..b0066fa75f22 100644
--- a/pkgs/development/libraries/libunique/3.x.nix
+++ b/pkgs/development/libraries/libunique/3.x.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     sha256 = "0f70lkw66v9cj72q0iw1s2546r6bwwcd8idcm3621fg2fgh2rw58";
   };
 
-  buildInputs = [ pkgconfig dbus dbus_glib gtk3 gobjectIntrospection gtkdoc docbook_xml_dtd_45 docbook_xsl libxslt libxml2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ dbus dbus_glib gtk3 gobjectIntrospection gtkdoc docbook_xml_dtd_45 docbook_xsl libxslt libxml2 ];
 
   meta = {
     homepage = https://wiki.gnome.org/Attic/LibUnique;
diff --git a/pkgs/development/libraries/libunique/default.nix b/pkgs/development/libraries/libunique/default.nix
index ebf81c67be05..a5adaa9ac179 100644
--- a/pkgs/development/libraries/libunique/default.nix
+++ b/pkgs/development/libraries/libunique/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
     ./1.1.6-include-terminator.patch
   ];
 
-  buildInputs = [ pkgconfig glib gtk2 dbus_glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib gtk2 dbus_glib ];
 
   # don't make deprecated usages hard errors
   preBuild = ''substituteInPlace unique/dbus/Makefile --replace -Werror ""'';
diff --git a/pkgs/development/libraries/libvdpau/default.nix b/pkgs/development/libraries/libvdpau/default.nix
index 79863f40dffb..ceb42fe2bfc3 100644
--- a/pkgs/development/libraries/libvdpau/default.nix
+++ b/pkgs/development/libraries/libvdpau/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" ];
 
-  buildInputs = with xorg; [ pkgconfig dri2proto libXext ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = with xorg; [ dri2proto libXext ];
 
   propagatedBuildInputs = [ xorg.libX11 ];
 
diff --git a/pkgs/development/libraries/libviper/default.nix b/pkgs/development/libraries/libviper/default.nix
index 90c1f07da5ae..6ca3d997e659 100644
--- a/pkgs/development/libraries/libviper/default.nix
+++ b/pkgs/development/libraries/libviper/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
     mkdir -p $out/lib
   '';
 
-  buildInputs = [pkgconfig glib ncurses gpm];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ncurses gpm];
 
   meta = with stdenv.lib; {
     homepage = http://libviper.sourceforge.net/;
diff --git a/pkgs/development/libraries/libvisual/default.nix b/pkgs/development/libraries/libvisual/default.nix
index 50a4c7c8f247..8bac0f41ddeb 100644
--- a/pkgs/development/libraries/libvisual/default.nix
+++ b/pkgs/development/libraries/libvisual/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1my1ipd5k1ixag96kwgf07bgxkjlicy9w22jfxb2kq95f6wgsk8b";
   };
 
-  buildInputs = [ pkgconfig glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ];
 
   hardeningDisable = [ "format" ];
 
diff --git a/pkgs/development/libraries/libvterm/default.nix b/pkgs/development/libraries/libvterm/default.nix
index e58d964a6253..472539ea24bb 100644
--- a/pkgs/development/libraries/libvterm/default.nix
+++ b/pkgs/development/libraries/libvterm/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     mkdir -p $out/lib
   '';
 
-  buildInputs = [ pkgconfig glib ncurses ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ncurses ];
 
   meta = with stdenv.lib; {
     homepage = http://libvterm.sourceforge.net/;
diff --git a/pkgs/development/libraries/libwmf/default.nix b/pkgs/development/libraries/libwmf/default.nix
index 5683e88b0205..eed0c77af804 100644
--- a/pkgs/development/libraries/libwmf/default.nix
+++ b/pkgs/development/libraries/libwmf/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "1y3wba4q8pl7kr51212jwrsz1x6nslsx1gsjml1x0i8549lmqd2v";
   };
 
-  buildInputs = [ zlib imagemagick libpng pkgconfig glib freetype libjpeg libxml2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zlib imagemagick libpng glib freetype libjpeg libxml2 ];
 
   patches = [
     ./CVE-2006-3376.patch ./CVE-2009-1364.patch
diff --git a/pkgs/development/libraries/libwnck/3.x.nix b/pkgs/development/libraries/libwnck/3.x.nix
index 094edc36bbbf..ed775fb45932 100644
--- a/pkgs/development/libraries/libwnck/3.x.nix
+++ b/pkgs/development/libraries/libwnck/3.x.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
 
   patches = [ ./install_introspection_to_prefix.patch ];
 
-  buildInputs = [ pkgconfig intltool ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ intltool ];
   propagatedBuildInputs = [ libX11 gtk3 ];
 
   meta = {
diff --git a/pkgs/development/libraries/libwnck/default.nix b/pkgs/development/libraries/libwnck/default.nix
index 6e0809664cff..254541374104 100644
--- a/pkgs/development/libraries/libwnck/default.nix
+++ b/pkgs/development/libraries/libwnck/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
   outputs = [ "out" "dev" "devdoc" ];
   outputBin = "dev";
 
-  buildInputs = [ pkgconfig gtk2 intltool xorg.libX11 xorg.libXres ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 intltool xorg.libX11 xorg.libXres ];
   # ?another optional: startup-notification
 
   configureFlags = [ "--disable-introspection" ]; # not needed anywhere AFAIK
diff --git a/pkgs/development/libraries/libwps/default.nix b/pkgs/development/libraries/libwps/default.nix
index b165631e23eb..73fe5b55ab45 100644
--- a/pkgs/development/libraries/libwps/default.nix
+++ b/pkgs/development/libraries/libwps/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0v1a0hj96i4jhb5833336s4zcslzb6md5cnmnrvgywx8cmw40c0c";
   };
 
-  buildInputs = [ boost pkgconfig librevenge zlib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ boost librevenge zlib ];
 
   meta = with stdenv.lib; {
     homepage = http://libwps.sourceforge.net/;
diff --git a/pkgs/development/libraries/libxkbcommon/default.nix b/pkgs/development/libraries/libxkbcommon/default.nix
index 486d52a2e27b..fd61ae840284 100644
--- a/pkgs/development/libraries/libxkbcommon/default.nix
+++ b/pkgs/development/libraries/libxkbcommon/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" ];
 
-  buildInputs = [ pkgconfig yacc flex xkeyboard_config libxcb ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ yacc flex xkeyboard_config libxcb ];
 
   configureFlags = [
     "--with-xkb-config-root=${xkeyboard_config}/etc/X11/xkb"
diff --git a/pkgs/development/libraries/luaffi/default.nix b/pkgs/development/libraries/luaffi/default.nix
index 38dfba4c462c..1e4cf11d1fa0 100644
--- a/pkgs/development/libraries/luaffi/default.nix
+++ b/pkgs/development/libraries/luaffi/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "1hv1y9i66p473hfy36nqj220sfrxdmbd75c1gpjvpk8073vx55ac";
   };
 
-  buildInputs = [ lua pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ lua ];
 
   patches = [
     ./makefile-errors.patch
diff --git a/pkgs/development/libraries/mediastreamer/msopenh264.nix b/pkgs/development/libraries/mediastreamer/msopenh264.nix
index 47b7029927cf..bc5dda6cff1b 100644
--- a/pkgs/development/libraries/mediastreamer/msopenh264.nix
+++ b/pkgs/development/libraries/mediastreamer/msopenh264.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "001km4xy1ifwbg1c19ncc75h867fzfcxy9pxvl4pxqb64169xc1k";
   };
 
-  buildInputs = [ autoreconfHook pkgconfig mediastreamer openh264 ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ mediastreamer openh264 ];
   nativeBuildInputs = [ cmake ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/mongoc/default.nix b/pkgs/development/libraries/mongoc/default.nix
index 67d2bdf1559b..ff3ec3df5ed7 100644
--- a/pkgs/development/libraries/mongoc/default.nix
+++ b/pkgs/development/libraries/mongoc/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
   };
 
   propagatedBuildInputs = [ libbson ];
-  buildInputs = [ openssl perl pkgconfig which ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ openssl perl which ];
 
   meta = with stdenv.lib; {
     description = "The official C client library for MongoDB";
diff --git a/pkgs/development/libraries/mono-zeroconf/default.nix b/pkgs/development/libraries/mono-zeroconf/default.nix
index 12b15c4937d7..444ec9dac2be 100644
--- a/pkgs/development/libraries/mono-zeroconf/default.nix
+++ b/pkgs/development/libraries/mono-zeroconf/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1qfp4qvsx7rc2shj1chi2y7fxn10rwi70rw2y54b2i8a4jq7gpkb";
   };
 
-  buildInputs = [ pkgconfig which mono ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ which mono ];
 
   dontStrip = true;
 
diff --git a/pkgs/development/libraries/movit/default.nix b/pkgs/development/libraries/movit/default.nix
index a344b8fa92f4..d85d4f444077 100644
--- a/pkgs/development/libraries/movit/default.nix
+++ b/pkgs/development/libraries/movit/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
 
   propagatedBuildInputs = [ eigen epoxy ];
 
-  buildInputs = [ SDL fftw gtest pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ SDL fftw gtest ];
 
   meta = with stdenv.lib; {
     description = "High-performance, high-quality video filters for the GPU";
diff --git a/pkgs/development/libraries/mps/default.nix b/pkgs/development/libraries/mps/default.nix
index 852946e7e40f..4e4ddfb63899 100644
--- a/pkgs/development/libraries/mps/default.nix
+++ b/pkgs/development/libraries/mps/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1k7vnanpgawnj84x2xs6md57pfib9p7c3acngqzkl3c2aqw8qay0";
   };
 
-  buildInputs = [ autoreconfHook sqlite ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ sqlite ];
 
   meta = {
     description = "A flexible memory management and garbage collection library";
diff --git a/pkgs/development/libraries/mygui/default.nix b/pkgs/development/libraries/mygui/default.nix
index 6e4b3e6a862a..715d2cb90f47 100644
--- a/pkgs/development/libraries/mygui/default.nix
+++ b/pkgs/development/libraries/mygui/default.nix
@@ -16,7 +16,8 @@ in stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [ libX11 unzip cmake ois freetype libuuid boost pkgconfig (if withOgre then ogre else mesa) ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libX11 unzip cmake ois freetype libuuid boost (if withOgre then ogre else mesa) ];
 
   # Tools are disabled due to compilation failures.
   cmakeFlags = [ "-DMYGUI_BUILD_TOOLS=OFF" "-DMYGUI_BUILD_DEMOS=OFF" "-DMYGUI_RENDERSYSTEM=${renderSystem}" ];
diff --git a/pkgs/development/libraries/ndn-cxx/default.nix b/pkgs/development/libraries/ndn-cxx/default.nix
index 8df9715a4f4a..ee7d4765fb22 100644
--- a/pkgs/development/libraries/ndn-cxx/default.nix
+++ b/pkgs/development/libraries/ndn-cxx/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     rev = "4c32e748863d5165cc0e3d6b54a8383f4836cdf1";
     sha256 = "18szs3j3ig8wlcqngran0daxaj7j2qsmch0212ids6fymj1hgax4";
   };
-  buildInputs = [ openssl doxygen boost sqlite cryptopp pkgconfig python pythonPackages.sphinx];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ openssl doxygen boost sqlite cryptopp python pythonPackages.sphinx];
   preConfigure = ''
     patchShebangs waf
     ./waf configure \
diff --git a/pkgs/development/libraries/neardal/default.nix b/pkgs/development/libraries/neardal/default.nix
index 9f46305c1b54..e0adb312677c 100644
--- a/pkgs/development/libraries/neardal/default.nix
+++ b/pkgs/development/libraries/neardal/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "12qwg7qiw2wfpaxfg2fjkmj5lls0g33xp6w433g8bnkvwlq4s29g";
   };
 
-  buildInputs = [ autoconf automake libtool pkgconfig glib readline makeWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool glib readline makeWrapper ];
 
   preConfigure = ''
     substituteInPlace "ncl/Makefile.am" --replace "noinst_PROGRAMS" "bin_PROGRAMS"
diff --git a/pkgs/development/libraries/neon/0.29.nix b/pkgs/development/libraries/neon/0.29.nix
index fbd0c053f047..e393d50bf9d2 100644
--- a/pkgs/development/libraries/neon/0.29.nix
+++ b/pkgs/development/libraries/neon/0.29.nix
@@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
 
   patches = optionals stdenv.isDarwin [ ./0.29.6-darwin-fix-configure.patch ];
 
-  buildInputs = [libxml2 pkgconfig openssl]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [libxml2 openssl]
     ++ stdenv.lib.optional compressionSupport zlib;
 
   configureFlags = ''
diff --git a/pkgs/development/libraries/neon/default.nix b/pkgs/development/libraries/neon/default.nix
index e0156be5da52..2351e3b0800b 100644
--- a/pkgs/development/libraries/neon/default.nix
+++ b/pkgs/development/libraries/neon/default.nix
@@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
 
   patches = optionals stdenv.isDarwin [ ./0.29.6-darwin-fix-configure.patch ];
 
-  buildInputs = [libxml2 pkgconfig openssl]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [libxml2 openssl]
     ++ stdenv.lib.optional compressionSupport zlib;
 
   configureFlags = ''
diff --git a/pkgs/development/libraries/nss_wrapper/default.nix b/pkgs/development/libraries/nss_wrapper/default.nix
index 8f3a313b21df..9051d96eff79 100644
--- a/pkgs/development/libraries/nss_wrapper/default.nix
+++ b/pkgs/development/libraries/nss_wrapper/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0bysdijvi9n0jk74iklbfhbp0kvv81a727lcfd5q03q2hkzjfm18";
   };
 
-  buildInputs = [ cmake pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake ];
 
   meta = with stdenv.lib; {
     description = "A wrapper for the user, group and hosts NSS API";
diff --git a/pkgs/development/libraries/opal/default.nix b/pkgs/development/libraries/opal/default.nix
index 36a4c3b0bb67..f86e4d120976 100644
--- a/pkgs/development/libraries/opal/default.nix
+++ b/pkgs/development/libraries/opal/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "f208985003461b2743575eccac13ad890b3e5baac35b68ddef17162460aff864";
   };
 
-  buildInputs = [ pkgconfig ptlib srtp libtheora speex
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ptlib srtp libtheora speex
                   ffmpeg x264 cyrus_sasl openldap openssl expat unixODBC ];
   propagatedBuildInputs = [ speex ]; 
 
diff --git a/pkgs/development/libraries/opencollada/default.nix b/pkgs/development/libraries/opencollada/default.nix
index 160599837c55..5ce30b039696 100644
--- a/pkgs/development/libraries/opencollada/default.nix
+++ b/pkgs/development/libraries/opencollada/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "0gpjvzcfyilb96x5ywajxgkw42ipwp4my36z9cq686bd9vpp3q0g";
   };
 
-  buildInputs = [ cmake pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake ];
 
   propagatedBuildInputs = [ libxml2 pcre ];
 
diff --git a/pkgs/development/libraries/openct/default.nix b/pkgs/development/libraries/openct/default.nix
index aafdd60e415f..5eb08ecd6014 100644
--- a/pkgs/development/libraries/openct/default.nix
+++ b/pkgs/development/libraries/openct/default.nix
@@ -25,7 +25,8 @@ stdenv.mkDerivation rec {
     "--sysconfdir=/etc"
   ];
 
-  buildInputs = [ autoreconfHook pkgconfig pcsclite libusb doxygen libxslt ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ pcsclite libusb doxygen libxslt ];
 
   preInstall = ''
     mkdir -p $out/etc
diff --git a/pkgs/development/libraries/openexr/default.nix b/pkgs/development/libraries/openexr/default.nix
index 22cc5b416e7d..27a9860c8683 100644
--- a/pkgs/development/libraries/openexr/default.nix
+++ b/pkgs/development/libraries/openexr/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
     ./bootstrap
   '';
 
-  buildInputs = [ autoconf automake libtool pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool ];
   propagatedBuildInputs = [ ilmbase zlib ];
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/openwsman/default.nix b/pkgs/development/libraries/openwsman/default.nix
index 0eb940c119ea..b179ca8803c1 100644
--- a/pkgs/development/libraries/openwsman/default.nix
+++ b/pkgs/development/libraries/openwsman/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0gw2dsjxzpchg3s85kplwgp9xhd9l7q4fh37iy7r203pvir4k6s4";
   };
 
-  buildInputs = [ autoconf automake libtool pkgconfig libxml2 curl cmake pam sblim-sfcc ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf automake libtool libxml2 curl cmake pam sblim-sfcc ];
 
   cmakeFlags = [
     "-DCMAKE_BUILD_RUBY_GEM=no"
diff --git a/pkgs/development/libraries/pangox-compat/default.nix b/pkgs/development/libraries/pangox-compat/default.nix
index eb3c12023678..8154fca29e84 100644
--- a/pkgs/development/libraries/pangox-compat/default.nix
+++ b/pkgs/development/libraries/pangox-compat/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0ip0ziys6mrqqmz4n71ays0kf5cs1xflj1gfpvs4fgy2nsrr482m";
   };
 
-  buildInputs = [ pkgconfig glib pango libX11 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib pango libX11 ];
 
   meta = {
     description = "A compatibility library for pango>1.30.*";
diff --git a/pkgs/development/libraries/pcl/default.nix b/pkgs/development/libraries/pcl/default.nix
index b9762e284e68..6b8ba68adb76 100644
--- a/pkgs/development/libraries/pcl/default.nix
+++ b/pkgs/development/libraries/pcl/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [ cmake qhull flann boost eigen pkgconfig libusb1 libpcap
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake qhull flann boost eigen libusb1 libpcap
                   libpng vtk qt4 libXt ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa AGL cf-private ];
   cmakeFlags = stdenv.lib.optionals stdenv.isDarwin [
diff --git a/pkgs/development/libraries/pkcs11helper/default.nix b/pkgs/development/libraries/pkcs11helper/default.nix
index f59c538856ca..9d7d7552cfc7 100644
--- a/pkgs/development/libraries/pkcs11helper/default.nix
+++ b/pkgs/development/libraries/pkcs11helper/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "17a2cssycl7fh44xikmhszigx57vvn0h2sjsnmsy3772kfj796b1";
   };
 
-  buildInputs = [ pkgconfig openssl autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ openssl ];
 
   meta = with stdenv.lib; {
     homepage = https://www.opensc-project.org/opensc/wiki/pkcs11-helper;
diff --git a/pkgs/development/libraries/pocketsphinx/default.nix b/pkgs/development/libraries/pocketsphinx/default.nix
index bc37cfb3d184..f892540ae5c1 100644
--- a/pkgs/development/libraries/pocketsphinx/default.nix
+++ b/pkgs/development/libraries/pocketsphinx/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation rec {
 
   propagatedBuildInputs = [ sphinxbase ];
 
-  buildInputs = [ pkgconfig python27 swig2 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python27 swig2 ];
 
   meta = {
     description = "Voice recognition library written in C";
diff --git a/pkgs/development/libraries/portaudio/default.nix b/pkgs/development/libraries/portaudio/default.nix
index 41f29a1a6b19..c55d17113219 100644
--- a/pkgs/development/libraries/portaudio/default.nix
+++ b/pkgs/development/libraries/portaudio/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "04qmin6nj144b8qb9kkd9a52xfvm0qdgm8bg8jbl7s3frmyiv8pm";
   };
 
-  buildInputs = [ pkgconfig libjack2 ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libjack2 ]
     ++ stdenv.lib.optional (!stdenv.isDarwin) alsaLib;
 
   configureFlags = [ "--disable-mac-universal" ];
diff --git a/pkgs/development/libraries/protobuf/generic-v3.nix b/pkgs/development/libraries/protobuf/generic-v3.nix
index 44ecdcb2f659..269417959061 100644
--- a/pkgs/development/libraries/protobuf/generic-v3.nix
+++ b/pkgs/development/libraries/protobuf/generic-v3.nix
@@ -28,7 +28,8 @@ stdenv.mkDerivation rec {
       --replace 'tmpnam(b)' '"'$TMPDIR'/foo"'
   '';
 
-  buildInputs = [ autoreconfHook zlib ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ zlib ];
 
   enableParallelBuilding = true;
 
diff --git a/pkgs/development/libraries/protobuf/generic.nix b/pkgs/development/libraries/protobuf/generic.nix
index b7c456df85c4..06154e0008ba 100644
--- a/pkgs/development/libraries/protobuf/generic.nix
+++ b/pkgs/development/libraries/protobuf/generic.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "lib" ];
 
-  buildInputs = [ autoreconfHook zlib ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ zlib ];
 
   # The generated C++ code uses static initializers which mutate a global data
   # structure. This causes problems for an executable when:
diff --git a/pkgs/development/libraries/protobufc/generic.nix b/pkgs/development/libraries/protobufc/generic.nix
index 3a03d5c8b4b2..b9ad506e20a8 100644
--- a/pkgs/development/libraries/protobufc/generic.nix
+++ b/pkgs/development/libraries/protobufc/generic.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
 
   inherit src;
 
-  buildInputs = [ autoreconfHook pkgconfig protobuf zlib ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ protobuf zlib ];
 
   meta = with stdenv.lib; {
     homepage = http://github.com/protobuf-c/protobuf-c/;
diff --git a/pkgs/development/libraries/ptlib/default.nix b/pkgs/development/libraries/ptlib/default.nix
index ecea72d2e8f8..c5d3d7411309 100644
--- a/pkgs/development/libraries/ptlib/default.nix
+++ b/pkgs/development/libraries/ptlib/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
 
   NIX_CFLAGS_COMPILE = "-std=gnu++98";
 
-  buildInputs = [ pkgconfig bison flex unixODBC openssl openldap
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ bison flex unixODBC openssl openldap
                   cyrus_sasl kerberos expat SDL libdv libv4l alsaLib ];
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/qt-5/5.9/qtmultimedia.nix b/pkgs/development/libraries/qt-5/5.9/qtmultimedia.nix
index e133256e9004..4fe9c90232a2 100644
--- a/pkgs/development/libraries/qt-5/5.9/qtmultimedia.nix
+++ b/pkgs/development/libraries/qt-5/5.9/qtmultimedia.nix
@@ -8,7 +8,8 @@ with stdenv.lib;
 qtSubmodule {
   name = "qtmultimedia";
   qtInputs = [ qtbase qtdeclarative ];
-  buildInputs = [ pkgconfig gstreamer gst-plugins-base libpulseaudio]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gstreamer gst-plugins-base libpulseaudio]
     ++ optional (stdenv.isLinux) alsaLib;
   outputs = [ "out" "dev" "bin" ];
   qmakeFlags = [ "GST_VERSION=1.0" ];
diff --git a/pkgs/development/libraries/rdkafka/default.nix b/pkgs/development/libraries/rdkafka/default.nix
index 1bd7305867dd..ff017279dc64 100644
--- a/pkgs/development/libraries/rdkafka/default.nix
+++ b/pkgs/development/libraries/rdkafka/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0yp8vmj3yc564hcmhx46ssyn8qayywnsrg4wg67qk6jw967qgwsn";
   };
 
-  buildInputs = [ zlib perl pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ zlib perl python ];
 
   NIX_CFLAGS_COMPILE = "-Wno-error=strict-overflow";
 
diff --git a/pkgs/development/libraries/rep-gtk/default.nix b/pkgs/development/libraries/rep-gtk/default.nix
index bb709e952f8b..5629164f160a 100644
--- a/pkgs/development/libraries/rep-gtk/default.nix
+++ b/pkgs/development/libraries/rep-gtk/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "0hgkkywm8zczir3lqr727bn7ybgg71x9cwj1av8fykkr8pdpard9";
   };
 
-  buildInputs = [ pkgconfig autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ];
   propagatedBuildInputs = [ librep gtk2 ];
 
   patchPhase = ''
diff --git a/pkgs/development/libraries/rubberband/default.nix b/pkgs/development/libraries/rubberband/default.nix
index b0707ad15f06..364a4d4794a8 100644
--- a/pkgs/development/libraries/rubberband/default.nix
+++ b/pkgs/development/libraries/rubberband/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "0x9bm2nqd6w2f35w2sqcp7h5z34i4w7mdg53m0vzjhffnnq6637z";
   };
 
-  buildInputs = [ pkgconfig libsamplerate libsndfile fftw vampSDK ladspaH ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libsamplerate libsndfile fftw vampSDK ladspaH ];
 
   meta = with stdenv.lib; {
     description = "High quality software library for audio time-stretching and pitch-shifting";
diff --git a/pkgs/development/libraries/serd/default.nix b/pkgs/development/libraries/serd/default.nix
index 0023427f1bab..968550675235 100644
--- a/pkgs/development/libraries/serd/default.nix
+++ b/pkgs/development/libraries/serd/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "164j43am4hka2vbzw4n52zy7rafgp6kmkgbcbvap368az644mr73";
   };
 
-  buildInputs = [ pcre pkgconfig python ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ pcre python ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/shibboleth-sp/default.nix b/pkgs/development/libraries/shibboleth-sp/default.nix
index f15c72498b25..4bdc9503c9af 100644
--- a/pkgs/development/libraries/shibboleth-sp/default.nix
+++ b/pkgs/development/libraries/shibboleth-sp/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "1b5r4nd098lnjwr2g13f04ycqv5fvbrhpwg6fsdk8xy9cigvfzxj";
   };
 
-  buildInputs = [ boost fcgi openssl opensaml-cpp log4shib pkgconfig xercesc xml-security-c xml-tooling-c ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ boost fcgi openssl opensaml-cpp log4shib xercesc xml-security-c xml-tooling-c ];
   nativeBuildInputs = [ autoreconfHook ];
 
   configureFlags = [
diff --git a/pkgs/development/libraries/silgraphite/default.nix b/pkgs/development/libraries/silgraphite/default.nix
new file mode 100644
index 000000000000..9d0aca0ab14b
--- /dev/null
+++ b/pkgs/development/libraries/silgraphite/default.nix
@@ -0,0 +1,22 @@
+{ stdenv, fetchurl, pkgconfig, freetype, libXft, pango, fontconfig }:
+
+stdenv.mkDerivation rec {
+  version = "2.3.1";
+  name = "silgraphite-2.3.1";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/silgraphite/silgraphite/${version}/${name}.tar.gz";
+    sha256 = "9b07c6e91108b1fa87411af4a57e25522784cfea0deb79b34ced608444f2ed65";
+  };
+
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ freetype libXft pango fontconfig];
+
+  NIX_CFLAGS_COMPILE = "-I${freetype.dev}/include/freetype2";
+
+  meta = {
+    description = "An advanced font engine";
+    maintainers = [ stdenv.lib.maintainers.raskin ];
+    platforms = stdenv.lib.platforms.linux;
+  };
+}
diff --git a/pkgs/development/libraries/silgraphite/graphite2.nix b/pkgs/development/libraries/silgraphite/graphite2.nix
index a399db1b71f8..a5dc1f41e984 100644
--- a/pkgs/development/libraries/silgraphite/graphite2.nix
+++ b/pkgs/development/libraries/silgraphite/graphite2.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0xdg6bc02bl8yz39l5i2skczfg17q4lif0qqan0dhvk0mibpcpj7";
   };
 
-  buildInputs = [ pkgconfig freetype cmake ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ freetype cmake ];
 
   patches = stdenv.lib.optionals stdenv.isDarwin [ ./macosx.patch ];
 
diff --git a/pkgs/development/libraries/snack/default.nix b/pkgs/development/libraries/snack/default.nix
index 9bae9feb693e..17195febe133 100644
--- a/pkgs/development/libraries/snack/default.nix
+++ b/pkgs/development/libraries/snack/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation {
 
   postUnpack = ''sourceRoot="$sourceRoot/unix"'';
 
-  buildInputs = [ python tcl tk vorbis-tools pkgconfig xlibsWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python tcl tk vorbis-tools xlibsWrapper ];
 
   hardeningDisable = [ "format" ];
 
diff --git a/pkgs/development/libraries/sord/default.nix b/pkgs/development/libraries/sord/default.nix
index 01ea4c4a1626..57f81aa4613e 100644
--- a/pkgs/development/libraries/sord/default.nix
+++ b/pkgs/development/libraries/sord/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0nh3i867g9z4kdlnk82cg2kcw8r02qgifxvkycvzb4vfjv4v4g4x";
   };
 
-  buildInputs = [ pkgconfig python serd ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python serd ];
 
   configurePhase = "${python.interpreter} waf configure --prefix=$out";
 
diff --git a/pkgs/development/libraries/spatialite-tools/default.nix b/pkgs/development/libraries/spatialite-tools/default.nix
index 6f7d154bbe83..ff461f1b8e64 100644
--- a/pkgs/development/libraries/spatialite-tools/default.nix
+++ b/pkgs/development/libraries/spatialite-tools/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "14aqmhvab63ydbb82fglsbig7jw1wmci8jjvci07aavdhvh1pyrv";
   };
 
-  buildInputs = [ pkgconfig sqlite expat zlib proj geos libspatialite readosm ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ sqlite expat zlib proj geos libspatialite readosm ];
 
   configureFlags = "--disable-freexl";
 
diff --git a/pkgs/development/libraries/sphinxbase/default.nix b/pkgs/development/libraries/sphinxbase/default.nix
index e82b2fe045b3..57c3ae40fd97 100644
--- a/pkgs/development/libraries/sphinxbase/default.nix
+++ b/pkgs/development/libraries/sphinxbase/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation (rec {
     sha256 = "0vr4k8pv5a8nvq9yja7kl13b5lh0f9vha8fc8znqnm8bwmcxnazp";
   };
 
-  buildInputs = [ swig2 python27 pkgconfig bison ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ swig2 python27 bison ];
 
   meta = {
     description = "Support Library for Pocketsphinx";
diff --git a/pkgs/development/libraries/startup-notification/default.nix b/pkgs/development/libraries/startup-notification/default.nix
index b4b29b54881e..ce4fca6da70d 100644
--- a/pkgs/development/libraries/startup-notification/default.nix
+++ b/pkgs/development/libraries/startup-notification/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation {
     sha256 = "3c391f7e930c583095045cd2d10eb73a64f085c7fde9d260f2652c7cb3cfbe4a";
   };
 
-  buildInputs = [ libX11 libxcb pkgconfig xcbutil ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libX11 libxcb xcbutil ];
 
   meta = {
     homepage = http://www.freedesktop.org/software/startup-notification;
diff --git a/pkgs/development/libraries/subunit/default.nix b/pkgs/development/libraries/subunit/default.nix
index e4a767579ab7..35bacff0525a 100644
--- a/pkgs/development/libraries/subunit/default.nix
+++ b/pkgs/development/libraries/subunit/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0lcah7p66c05p7xpw6ns1is0i02lh0nq8gq51mv4wyvbr6zaasa8";
   };
 
-  buildInputs = [ pkgconfig check cppunit perl pythonPackages.wrapPython ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ check cppunit perl pythonPackages.wrapPython ];
 
   propagatedBuildInputs = with pythonPackages; [ testtools testscenarios ];
 
diff --git a/pkgs/development/libraries/svrcore/default.nix b/pkgs/development/libraries/svrcore/default.nix
index ddb880e6bf27..f1ae1ea5db0e 100644
--- a/pkgs/development/libraries/svrcore/default.nix
+++ b/pkgs/development/libraries/svrcore/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0n3alg6bxml8952fb6h0bi0l29farvq21q6k20gy2ba90m3znwj7";
   };
 
-  buildInputs = [ pkgconfig nss nspr ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ nss nspr ];
 
   meta = with stdenv.lib; {
     description = "Secure PIN handling using NSS crypto";
diff --git a/pkgs/development/libraries/sword/default.nix b/pkgs/development/libraries/sword/default.nix
index 44f6cabd35a7..13497f7727f4 100644
--- a/pkgs/development/libraries/sword/default.nix
+++ b/pkgs/development/libraries/sword/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0g91kpfkwccvdikddffdbzd6glnp1gdvkx4vh04iyz10bb7shpcr";
   };
 
-  buildInputs = [ pkgconfig icu clucene_core curl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ icu clucene_core curl ];
 
   prePatch = ''
     patchShebangs .;
diff --git a/pkgs/development/libraries/telepathy/glib/default.nix b/pkgs/development/libraries/telepathy/glib/default.nix
index bc9e861df9c6..ec26c9f567b5 100644
--- a/pkgs/development/libraries/telepathy/glib/default.nix
+++ b/pkgs/development/libraries/telepathy/glib/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
   LC_ALL = "en_US.UTF-8";
   propagatedBuildInputs = [dbus_glib glib gobjectIntrospection];
 
-  buildInputs = [pkgconfig libxslt glibcLocales python2 ] ++ stdenv.lib.optional valaSupport vala_0_23;
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxslt glibcLocales python2 ] ++ stdenv.lib.optional valaSupport vala_0_23;
 
   preConfigure = ''
     substituteInPlace telepathy-glib/telepathy-glib.pc.in --replace Requires.private Requires
diff --git a/pkgs/development/libraries/tk/generic.nix b/pkgs/development/libraries/tk/generic.nix
index 2258f28b9c48..843c6157479e 100644
--- a/pkgs/development/libraries/tk/generic.nix
+++ b/pkgs/development/libraries/tk/generic.nix
@@ -23,7 +23,8 @@ stdenv.mkDerivation {
     "--with-tcl=${tcl}/lib"
   ];
 
-  buildInputs = [ pkgconfig ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ]
     ++ stdenv.lib.optional stdenv.isDarwin fontconfig;
 
   propagatedBuildInputs = [ tcl libXft ];
diff --git a/pkgs/development/libraries/uhttpmock/default.nix b/pkgs/development/libraries/uhttpmock/default.nix
index 94223378151b..26c040721bdf 100644
--- a/pkgs/development/libraries/uhttpmock/default.nix
+++ b/pkgs/development/libraries/uhttpmock/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0kkf670abkq5ikm3mqls475lydfsd9by1kv5im4k757xrl1br1d4";
   };
 
-  buildInputs = [ autoconf gtk_doc automake libtool pkgconfig glib libsoup gobjectIntrospection ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ autoconf gtk_doc automake libtool glib libsoup gobjectIntrospection ];
 
   preConfigure = "./autogen.sh";
 
diff --git a/pkgs/development/libraries/unibilium/default.nix b/pkgs/development/libraries/unibilium/default.nix
index cf34c96a2fef..4742e2170131 100644
--- a/pkgs/development/libraries/unibilium/default.nix
+++ b/pkgs/development/libraries/unibilium/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
   makeFlags = [ "PREFIX=$(out)" ]
     ++ stdenv.lib.optional stdenv.isDarwin "LIBTOOL=${libtool}/bin/libtool";
 
-  buildInputs = [ libtool pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libtool ];
 
   meta = with lib; {
     description = "A very basic terminfo library";
diff --git a/pkgs/development/libraries/usbredir/default.nix b/pkgs/development/libraries/usbredir/default.nix
index f4ec02422242..e4e053805af7 100644
--- a/pkgs/development/libraries/usbredir/default.nix
+++ b/pkgs/development/libraries/usbredir/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
   # Works around bunch of "format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64_t {aka long long unsigned int}'" warnings
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isi686 "-Wno-error=format";
 
-  buildInputs = [ pkgconfig libusb ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libusb ];
   propagatedBuildInputs = [ libusb ];
 
   outputs = [ "out" "dev" ];
diff --git a/pkgs/development/libraries/vaapi-vdpau/default.nix b/pkgs/development/libraries/vaapi-vdpau/default.nix
index c7b8ddd8d6f0..4522ecc1bb63 100644
--- a/pkgs/development/libraries/vaapi-vdpau/default.nix
+++ b/pkgs/development/libraries/vaapi-vdpau/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
                           sha256 = "166svcav6axkrlb3i4rbf6dkwjnqdf69xw339az1f5yabj72pqqs";
                         }) ];
 
-  buildInputs = [ libvdpau mesa libva pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libvdpau mesa libva ];
 
   preConfigure = ''
     patch -p0 < ${libvdpau08patch}  # use -p0 instead of -p1
diff --git a/pkgs/development/libraries/vmmlib/default.nix b/pkgs/development/libraries/vmmlib/default.nix
index 3a7f8770e6c7..ee014fd46dac 100644
--- a/pkgs/development/libraries/vmmlib/default.nix
+++ b/pkgs/development/libraries/vmmlib/default.nix
@@ -3,7 +3,8 @@
 stdenv.mkDerivation rec {
   version = "1.6.2";
   name = "vmmlib-${version}";
-  buildInputs = [ stdenv pkgconfig cmake boost blas ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ stdenv cmake boost blas ];
 
   src = fetchFromGitHub {
     owner = "VMML";
diff --git a/pkgs/development/libraries/vulkan-loader/default.nix b/pkgs/development/libraries/vulkan-loader/default.nix
index f62279786c66..15a9e98b04e5 100644
--- a/pkgs/development/libraries/vulkan-loader/default.nix
+++ b/pkgs/development/libraries/vulkan-loader/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
   inherit version src;
 
   nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ cmake pkgconfig git python3 python3Packages.lxml
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake git python3 python3Packages.lxml
                   glslang spirv-tools x11 libxcb libXrandr libXext wayland
                 ];
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/wt/default.nix b/pkgs/development/libraries/wt/default.nix
index be661d0d270a..5d4caed890a8 100644
--- a/pkgs/development/libraries/wt/default.nix
+++ b/pkgs/development/libraries/wt/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [ cmake boost pkgconfig doxygen qt48Full libharu 
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake boost doxygen qt48Full libharu 
     pango fcgi firebird libmysql postgresql graphicsmagick glew 
     openssl pcre ];
 
diff --git a/pkgs/development/libraries/xml-security-c/default.nix b/pkgs/development/libraries/xml-security-c/default.nix
index 7ab6041e86dd..bbbf9af29e58 100644
--- a/pkgs/development/libraries/xml-security-c/default.nix
+++ b/pkgs/development/libraries/xml-security-c/default.nix
@@ -23,7 +23,8 @@ stdenv.mkDerivation rec {
     "--disable-static"
   ];
 
-  buildInputs = [ xalanc xercesc openssl pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ xalanc xercesc openssl ];
 
   meta = {
     homepage = http://santuario.apache.org/;
diff --git a/pkgs/development/libraries/xmlsec/default.nix b/pkgs/development/libraries/xmlsec/default.nix
index c64970f8f86e..8553e4b2a9a0 100644
--- a/pkgs/development/libraries/xmlsec/default.nix
+++ b/pkgs/development/libraries/xmlsec/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "1lpwj8dxwhha54sby0v5axjk79h56jnhjjiwiasbbk15vwzahz4n";
   };
 
-  buildInputs = [ makeWrapper libxml2 gnutls libxslt pkgconfig libgcrypt libtool openssl nss ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ makeWrapper libxml2 gnutls libxslt libgcrypt libtool openssl nss ];
   enableParallelBuilding = true;
   doCheck = true;
 
diff --git a/pkgs/development/libraries/zeitgeist/default.nix b/pkgs/development/libraries/zeitgeist/default.nix
index 252bcd02faff..e759e65dfc6b 100644
--- a/pkgs/development/libraries/zeitgeist/default.nix
+++ b/pkgs/development/libraries/zeitgeist/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
 
   configureFlags = [ "--with-session-bus-services-dir=$(out)/share/dbus-1/services" ];
 
-  buildInputs = [ pkgconfig glib sqlite gnome3.gnome_common intltool
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib sqlite gnome3.gnome_common intltool
                   libtool dbus_libs telepathy_glib vala_0_23 dbus_glib
                   gtk3 json_glib librdf_raptor2 python2Packages.rdflib ];
 
diff --git a/pkgs/development/libraries/zimg/default.nix b/pkgs/development/libraries/zimg/default.nix
index 961220bb7831..2c9d27a8b6ad 100644
--- a/pkgs/development/libraries/zimg/default.nix
+++ b/pkgs/development/libraries/zimg/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec{
     sha256 = "11pk8a5manr751jhy0xrql57jzab57lwqjxbpd8kvm9m8b51icwq";
   };
 
-  buildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ];
 
   meta = with stdenv.lib; {
     description = "Scaling, colorspace conversion and dithering library";
diff --git a/pkgs/development/mobile/adbfs-rootless/default.nix b/pkgs/development/mobile/adbfs-rootless/default.nix
index 38ecfcdf9a90..091d1adfefbc 100644
--- a/pkgs/development/mobile/adbfs-rootless/default.nix
+++ b/pkgs/development/mobile/adbfs-rootless/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  buildInputs = [ fuse pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ fuse ];
 
   postPatch = ''
     # very ugly way of replacing the adb calls
diff --git a/pkgs/development/ocaml-modules/ctypes/default.nix b/pkgs/development/ocaml-modules/ctypes/default.nix
index 24a67a38f3c3..b419971921ba 100644
--- a/pkgs/development/ocaml-modules/ctypes/default.nix
+++ b/pkgs/development/ocaml-modules/ctypes/default.nix
@@ -11,7 +11,8 @@ buildOcaml rec {
     sha256 = "164gyrs6zxr5pyljwpjgd4knwlrkcmamsq3gvkkkvgf9rmhrl3zf";
   };
 
-  buildInputs = [ ncurses pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ncurses ];
   propagatedBuildInputs = [ libffi ];
 
   hasSharedObjects = true;
diff --git a/pkgs/development/ocaml-modules/fontconfig/default.nix b/pkgs/development/ocaml-modules/fontconfig/default.nix
index 635572ea9c8f..4f586f2f99e0 100644
--- a/pkgs/development/ocaml-modules/fontconfig/default.nix
+++ b/pkgs/development/ocaml-modules/fontconfig/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "1fw6bzydmnyh2g4x35mcbg0hypnxqhynivk4nakcsx7prr8zr3yh";
   };
 
-  buildInputs = [ ocaml pkgconfig fontconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml fontconfig ];
   makeFlags = "OCAML_STDLIB_DIR=$(out)/lib/ocaml/${stdenv.lib.getVersion ocaml}/site-lib/ OCAML_HAVE_OCAMLOPT=yes";
 
   meta = {
diff --git a/pkgs/development/ocaml-modules/gmetadom/default.nix b/pkgs/development/ocaml-modules/gmetadom/default.nix
index 0f1facd65186..1d5aabf30046 100644
--- a/pkgs/development/ocaml-modules/gmetadom/default.nix
+++ b/pkgs/development/ocaml-modules/gmetadom/default.nix
@@ -22,7 +22,8 @@ stdenv.mkDerivation rec {
   '';
 
 
-  buildInputs = [ocaml findlib pkgconfig gdome2 libxslt];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ocaml findlib gdome2 libxslt];
   propagatedBuildInputs = [gdome2];
 
   meta = {
diff --git a/pkgs/development/ocaml-modules/lablgtk/2.14.0.nix b/pkgs/development/ocaml-modules/lablgtk/2.14.0.nix
index 2aa0842c55f7..5dc303b59f48 100644
--- a/pkgs/development/ocaml-modules/lablgtk/2.14.0.nix
+++ b/pkgs/development/ocaml-modules/lablgtk/2.14.0.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation (rec {
     sha256 = "1fnh0amm7lwgyjdhmlqgsp62gwlar1140425yc1j6inwmgnsp0a9";
   };
 
-  buildInputs = [ ocaml findlib pkgconfig gtk2 libgnomecanvas libglade gtksourceview camlp4 ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib gtk2 libgnomecanvas libglade gtksourceview camlp4 ];
 
   configureFlags = "--with-libdir=$(out)/lib/ocaml/${ocaml.version}/site-lib";
   buildFlags = "world";
diff --git a/pkgs/development/ocaml-modules/lablgtk/default.nix b/pkgs/development/ocaml-modules/lablgtk/default.nix
index 67f579eb4698..d6e56126018c 100644
--- a/pkgs/development/ocaml-modules/lablgtk/default.nix
+++ b/pkgs/development/ocaml-modules/lablgtk/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
     sha256 = "0cyj6sfdvzx8hw7553lhgwc0krlgvlza0ph3dk9gsxy047dm3wib";
   };
 
-  buildInputs = [ocaml findlib pkgconfig gtk2 libgnomecanvas libglade gtksourceview camlp4];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ocaml findlib gtk2 libgnomecanvas libglade gtksourceview camlp4];
 
   configureFlags = "--with-libdir=$(out)/lib/ocaml/${ocaml.version}/site-lib";
   buildFlags = "world";
diff --git a/pkgs/development/ocaml-modules/lablgtkmathview/default.nix b/pkgs/development/ocaml-modules/lablgtkmathview/default.nix
index 58e93b4f8374..b5bcb0de1ee6 100644
--- a/pkgs/development/ocaml-modules/lablgtkmathview/default.nix
+++ b/pkgs/development/ocaml-modules/lablgtkmathview/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
     sha256 = "0rgrpgwrgphw106l1xawxir002b7rmzc23rcxhv8ib6rymp1divx";
   };
 
-  buildInputs = [pkgconfig ocaml findlib gmetadom gtkmathview lablgtk];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib gmetadom gtkmathview lablgtk];
 
   createFindlibDestdir = true;
 
diff --git a/pkgs/development/ocaml-modules/lwt/default.nix b/pkgs/development/ocaml-modules/lwt/default.nix
index fc721dc4c9a3..99438cfc20c5 100644
--- a/pkgs/development/ocaml-modules/lwt/default.nix
+++ b/pkgs/development/ocaml-modules/lwt/default.nix
@@ -26,7 +26,8 @@ buildOcaml rec {
     inherit sha256;
   };
 
-  buildInputs = [ ocaml_oasis pkgconfig which cryptopp ocaml findlib ocamlbuild glib ncurses camlp4 cppo ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml_oasis which cryptopp ocaml findlib ocamlbuild glib ncurses camlp4 cppo ]
   ++ stdenv.lib.optional ppxSupport ppx_tools;
 
   propagatedBuildInputs = [ result ]
diff --git a/pkgs/development/ocaml-modules/ocaml-cairo/default.nix b/pkgs/development/ocaml-modules/ocaml-cairo/default.nix
index 80ae140a3fc4..165dda1fa027 100644
--- a/pkgs/development/ocaml-modules/ocaml-cairo/default.nix
+++ b/pkgs/development/ocaml-modules/ocaml-cairo/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
 
   patches = [ ./META.patch ];
 
-  buildInputs = [ ocaml automake gnum4 autoconf unzip pkgconfig
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml automake gnum4 autoconf unzip
                   findlib freetype lablgtk cairo gdk_pixbuf gtk2 pango ];
 
   createFindlibDestdir = true;
diff --git a/pkgs/development/ocaml-modules/ocaml-cairo2/default.nix b/pkgs/development/ocaml-modules/ocaml-cairo2/default.nix
index a4e4bf8674fe..d9cab2a759da 100644
--- a/pkgs/development/ocaml-modules/ocaml-cairo2/default.nix
+++ b/pkgs/development/ocaml-modules/ocaml-cairo2/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation {
     sha256 = "1lc1iv5yz49avbc0wbrw9nrx8dn0c35r7cykivjln1zc2fwscf7w";
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild pkgconfig cairo ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib ocamlbuild cairo ]
                 ++ optionals enableGtkSupport [ gtk2 ];
 
   # lablgtk2 is marked as a propagated build input since loading the
diff --git a/pkgs/development/ocaml-modules/ocamlnet/default.nix b/pkgs/development/ocaml-modules/ocamlnet/default.nix
index 51a30d7c91a2..9944cf821c50 100644
--- a/pkgs/development/ocaml-modules/ocamlnet/default.nix
+++ b/pkgs/development/ocaml-modules/ocamlnet/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation {
     sha256 = "0hhi3s4xas5i3p7214qfji5pvr7d30d89vnmkznxsfqj4v7dmhs6";
   };
 
-  buildInputs = [ ncurses ocaml findlib ocaml_pcre camlzip gnutls pkgconfig nettle ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ncurses ocaml findlib ocaml_pcre camlzip gnutls nettle ];
 
   createFindlibDestdir = true;
 
diff --git a/pkgs/development/ocaml-modules/ocamlsdl/default.nix b/pkgs/development/ocaml-modules/ocamlsdl/default.nix
index a5fd2d5076da..e8441cf6937c 100644
--- a/pkgs/development/ocaml-modules/ocamlsdl/default.nix
+++ b/pkgs/development/ocaml-modules/ocamlsdl/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
     sha256 = "abfb295b263dc11e97fffdd88ea1a28b46df8cc2b196777093e4fe7f509e4f8f";
   };
 
-  buildInputs = [ocaml pkgconfig findlib SDL SDL_image SDL_mixer SDL_ttf SDL_gfx lablgl];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ocaml findlib SDL SDL_image SDL_mixer SDL_ttf SDL_gfx lablgl];
 
   propagatedBuildInputs = [ SDL SDL_image SDL_mixer SDL_ttf SDL_gfx pkgconfig ];
   createFindlibDestdir = true;
diff --git a/pkgs/development/ocaml-modules/ocplib-simplex/default.nix b/pkgs/development/ocaml-modules/ocplib-simplex/default.nix
index 4ce3ac6dff30..eb25982a69b3 100644
--- a/pkgs/development/ocaml-modules/ocplib-simplex/default.nix
+++ b/pkgs/development/ocaml-modules/ocplib-simplex/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation {
     sha256 = "1fmz38w2cj9fny4adqqyil59dvndqkr59s7wk2gqs47r72b6sisa";
   };
 
-  buildInputs = [ autoreconfHook ocaml findlib ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ocaml findlib ];
 
   createFindlibDestdir = true;
 
diff --git a/pkgs/development/ocaml-modules/sqlite3/default.nix b/pkgs/development/ocaml-modules/sqlite3/default.nix
index cfa90226678a..38e1b3c7467d 100644
--- a/pkgs/development/ocaml-modules/sqlite3/default.nix
+++ b/pkgs/development/ocaml-modules/sqlite3/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0rwsx1nfa3xqmbygim2qx45jqm1gwf08m70wmcwkx50f1qk3l551";
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild pkgconfig sqlite ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib ocamlbuild sqlite ];
 
   createFindlibDestdir = true;
 
diff --git a/pkgs/development/ocaml-modules/tsdl/default.nix b/pkgs/development/ocaml-modules/tsdl/default.nix
index 01fa5b7ba6ab..1b90a539ac8c 100644
--- a/pkgs/development/ocaml-modules/tsdl/default.nix
+++ b/pkgs/development/ocaml-modules/tsdl/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation {
     sha256 = "13af37w2wybx8yzgjr5zz5l50402ldl614qiwphl1q69hig5mag2";
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild topkg result pkgconfig opam ocb-stubblr ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib ocamlbuild topkg result opam ocb-stubblr ];
   propagatedBuildInputs = [ SDL2 ctypes ];
 
   createFindlibDestdir = true;
diff --git a/pkgs/development/ocaml-modules/zarith/default.nix b/pkgs/development/ocaml-modules/zarith/default.nix
index 2cb4fdcd3014..5dc6a9056ada 100644
--- a/pkgs/development/ocaml-modules/zarith/default.nix
+++ b/pkgs/development/ocaml-modules/zarith/default.nix
@@ -23,7 +23,8 @@ stdenv.mkDerivation rec {
     inherit (param) url sha256;
   };
 
-  buildInputs = [ ocaml findlib pkgconfig perl ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ocaml findlib perl ];
   propagatedBuildInputs = [ gmp ];
 
   patchPhase = "patchShebangs ./z_pp.pl";
diff --git a/pkgs/development/pharo/vm/build-vm.nix b/pkgs/development/pharo/vm/build-vm.nix
index 7e80acb97c47..74fa75e7aa56 100644
--- a/pkgs/development/pharo/vm/build-vm.nix
+++ b/pkgs/development/pharo/vm/build-vm.nix
@@ -103,7 +103,8 @@ stdenv.mkDerivation rec {
   # http://forum.world.st/OSProcess-fork-issue-with-Debian-built-VM-td4947326.html
   #
   # (stack protection is disabled above for gcc 4.8 compatibility.)
-  buildInputs = [ bash unzip glibc openssl gcc48 mesa freetype xorg.libX11 xorg.libICE xorg.libSM alsaLib cairo pharo-share libuuid autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ bash unzip glibc openssl gcc48 mesa freetype xorg.libX11 xorg.libICE xorg.libSM alsaLib cairo pharo-share libuuid ];
 
   meta = {
     description = "Clean and innovative Smalltalk-inspired environment";
diff --git a/pkgs/development/pure-modules/doc/default.nix b/pkgs/development/pure-modules/doc/default.nix
index 68a083343752..54f99bf8afc9 100644
--- a/pkgs/development/pure-modules/doc/default.nix
+++ b/pkgs/development/pure-modules/doc/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "cfa880573941f37868269bcc443a09fecd2a141a78556383d2213f6c9f45ddd9";
   };
 
-  buildInputs = [ pkgconfig pure ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ pure ];
   makeFlags = "libdir=$(out)/lib prefix=$(out)/";
 
   meta = {
diff --git a/pkgs/development/pure-modules/gen/default.nix b/pkgs/development/pure-modules/gen/default.nix
index 082a8c88c61e..c29e508cc658 100644
--- a/pkgs/development/pure-modules/gen/default.nix
+++ b/pkgs/development/pure-modules/gen/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
   };
 
   hsEnv = haskellPackages.ghcWithPackages (hsPkgs : [hsPkgs.language-c]);
-  buildInputs = [ pkgconfig hsEnv pure ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ hsEnv pure ];
   makeFlags = "libdir=$(out)/lib prefix=$(out)/";
 
   meta = {
diff --git a/pkgs/development/pure-modules/pandoc/default.nix b/pkgs/development/pure-modules/pandoc/default.nix
index b51f2ff5e87a..d5b0a7dbde59 100644
--- a/pkgs/development/pure-modules/pandoc/default.nix
+++ b/pkgs/development/pure-modules/pandoc/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0f23a17549048ca3a8f4936ea9e931feb05997390b486850936b746996350cda";
   };
 
-  buildInputs = [ pkgconfig pure ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ pure ];
   propagatedBuildInputs = [ pandoc gawk getopt ];
   makeFlags = "libdir=$(out)/lib prefix=$(out)/";
   preInstall = ''
diff --git a/pkgs/development/python-modules/Cython/default.nix b/pkgs/development/python-modules/Cython/default.nix
index 22f3579bae3f..f94db1bdbe97 100644
--- a/pkgs/development/python-modules/Cython/default.nix
+++ b/pkgs/development/python-modules/Cython/default.nix
@@ -30,7 +30,8 @@ buildPythonPackage rec {
       tests/run/cpdef_enums.pyx
   '';
 
-  buildInputs = [ glibcLocales pkgconfig gdb ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glibcLocales gdb ];
   # For testing
   nativeBuildInputs = [ numpy ncurses ];
 
diff --git a/pkgs/development/python-modules/dbus/default.nix b/pkgs/development/python-modules/dbus/default.nix
index ab6e70a9a642..c8f122098da8 100644
--- a/pkgs/development/python-modules/dbus/default.nix
+++ b/pkgs/development/python-modules/dbus/default.nix
@@ -14,7 +14,8 @@ if isPyPy then throw "dbus-python not supported for interpreter ${python.executa
 
   postPatch = "patchShebangs .";
 
-  buildInputs = [ pkgconfig dbus dbus_glib ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ dbus dbus_glib ]
     ++ lib.optionals doCheck [ dbus_tools pygobject3 ]
     # My guess why it's sometimes trying to -lncurses.
     # It seems not to retain the dependency anyway.
diff --git a/pkgs/development/python-modules/graph-tool/2.x.x.nix b/pkgs/development/python-modules/graph-tool/2.x.x.nix
index 4f39d1097b1c..36181bfb3f95 100644
--- a/pkgs/development/python-modules/graph-tool/2.x.x.nix
+++ b/pkgs/development/python-modules/graph-tool/2.x.x.nix
@@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
     "--enable-openmp"
   ];
 
-  buildInputs = [ pkgconfig autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ];
 
   propagatedBuildInputs = [
     boost
diff --git a/pkgs/development/python-modules/h5py/default.nix b/pkgs/development/python-modules/h5py/default.nix
index 9b2821380b98..e9bae3f82060 100644
--- a/pkgs/development/python-modules/h5py/default.nix
+++ b/pkgs/development/python-modules/h5py/default.nix
@@ -28,7 +28,8 @@ in buildPythonPackage rec {
 
   preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";
 
-  buildInputs = [ hdf5 cython pkgconfig ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ hdf5 cython ]
     ++ optional mpiSupport mpi
     ;
   propagatedBuildInputs = [ numpy six]
diff --git a/pkgs/development/python-modules/pycairo/default.nix b/pkgs/development/python-modules/pycairo/default.nix
index 284736fd4754..b4366ab791f9 100644
--- a/pkgs/development/python-modules/pycairo/default.nix
+++ b/pkgs/development/python-modules/pycairo/default.nix
@@ -31,7 +31,8 @@ in buildPythonPackage rec {
     })
   ];
 
-  buildInputs = [ python pkgconfig cairo xlibsWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python cairo xlibsWrapper ];
 
   configurePhase = ''
     (
diff --git a/pkgs/development/python-modules/pygobject/3.nix b/pkgs/development/python-modules/pygobject/3.nix
index ce7210391c60..6afd10596bc6 100644
--- a/pkgs/development/python-modules/pygobject/3.nix
+++ b/pkgs/development/python-modules/pygobject/3.nix
@@ -13,7 +13,8 @@ buildPythonPackage rec {
 
   outputs = [ "out" "dev" ];
 
-  buildInputs = [ pkgconfig glib gobjectIntrospection ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib gobjectIntrospection ]
                  ++ stdenv.lib.optionals stdenv.isDarwin [ which ncurses ];
   propagatedBuildInputs = [ pycairo cairo ];
 
diff --git a/pkgs/development/python-modules/pygobject/default.nix b/pkgs/development/python-modules/pygobject/default.nix
index b72bd8b9b529..63a21cb2befd 100644
--- a/pkgs/development/python-modules/pygobject/default.nix
+++ b/pkgs/development/python-modules/pygobject/default.nix
@@ -20,7 +20,8 @@ buildPythonPackage rec {
 
   configureFlags = "--disable-introspection";
 
-  buildInputs = [ pkgconfig glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib ];
 
   # in a "normal" setup, pygobject and pygtk are installed into the
   # same site-packages: we need a pth file for both. pygtk.py would be
diff --git a/pkgs/development/python-modules/pygtk/default.nix b/pkgs/development/python-modules/pygtk/default.nix
index 0940ef00ac98..9b9adc64b755 100644
--- a/pkgs/development/python-modules/pygtk/default.nix
+++ b/pkgs/development/python-modules/pygtk/default.nix
@@ -11,7 +11,8 @@ buildPythonPackage rec {
     sha256 = "04k942gn8vl95kwf0qskkv6npclfm31d78ljkrkgyqxxcni1w76d";
   };
 
-  buildInputs = [ pkgconfig ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ ]
     ++ stdenv.lib.optional (libglade != null) libglade;
 
   propagatedBuildInputs = [ gtk2 pygobject2 pycairo ];
diff --git a/pkgs/development/python-modules/pygtksourceview/default.nix b/pkgs/development/python-modules/pygtksourceview/default.nix
index 499634236acd..7b89e6d1b28c 100644
--- a/pkgs/development/python-modules/pygtksourceview/default.nix
+++ b/pkgs/development/python-modules/pygtksourceview/default.nix
@@ -13,7 +13,8 @@ buildPythonPackage {
 
   patches = [ ./codegendir.patch ];
 
-  buildInputs = [ python pkgconfig pygobject2 glib pygtk gnome2.gtksourceview ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python pygobject2 glib pygtk gnome2.gtksourceview ];
 
   meta = {
     platforms = lib.platforms.unix;
diff --git a/pkgs/development/python-modules/pyqt/4.x.nix b/pkgs/development/python-modules/pyqt/4.x.nix
index cf1e17d3141b..b4376730e623 100644
--- a/pkgs/development/python-modules/pyqt/4.x.nix
+++ b/pkgs/development/python-modules/pyqt/4.x.nix
@@ -37,7 +37,8 @@ in buildPythonPackage {
     ${python.executable} configure.py $configureFlags "''${configureFlagsArray[@]}"
   '';
 
-  buildInputs = [ pkgconfig makeWrapper qt4 lndir dbus_libs ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ makeWrapper qt4 lndir dbus_libs ];
 
   propagatedBuildInputs = [ sip ];
 
diff --git a/pkgs/development/ruby-modules/gem-config/default.nix b/pkgs/development/ruby-modules/gem-config/default.nix
index bf1f9d14b776..2b0b43478aa2 100644
--- a/pkgs/development/ruby-modules/gem-config/default.nix
+++ b/pkgs/development/ruby-modules/gem-config/default.nix
@@ -39,7 +39,8 @@ let
 in
 
 {
-  atk = attrs: { buildInputs = [ gtk2 pcre pkgconfig ]; };
+  nativeBuildInputs = [ pkgconfig ];
+  atk = attrs: { buildInputs = [ gtk2 pcre ]; };
 
   bundler = attrs:
     let
@@ -57,7 +58,8 @@ in
     };
 
   cairo = attrs: {
-    buildInputs = [ gtk2 pcre pkgconfig xlibs.libpthreadstubs xlibs.libXdmcp];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ gtk2 pcre xlibs.libpthreadstubs xlibs.libXdmcp];
   };
 
   capybara-webkit = attrs: {
@@ -81,29 +83,35 @@ in
   };
 
   ffi = attrs: {
-    buildInputs = [ libffi pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ libffi ];
   };
 
   gpgme = attrs: {
     buildInputs = [ gpgme ];
   };
 
-  gio2 = attrs: { buildInputs = [ gtk2 pcre pkgconfig ]; };
+  nativeBuildInputs = [ pkgconfig ];
+  gio2 = attrs: { buildInputs = [ gtk2 pcre ]; };
 
   gitlab-markup = attrs: { meta.priority = 1; };
 
-  glib2 = attrs: { buildInputs = [ gtk2 pcre pkgconfig ]; };
+  nativeBuildInputs = [ pkgconfig ];
+  glib2 = attrs: { buildInputs = [ gtk2 pcre ]; };
 
   gtk2 = attrs: {
-    buildInputs = [ gtk2 pcre pkgconfig xlibs.libpthreadstubs xlibs.libXdmcp];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ gtk2 pcre xlibs.libpthreadstubs xlibs.libXdmcp];
     # CFLAGS must be set for this gem to detect gdkkeysyms.h correctly
     CFLAGS = "-I${gtk2.dev}/include/gtk-2.0 -I/non-existent-path";
   };
 
-  gobject-introspection = attrs: { buildInputs = [ gtk2 pcre pkgconfig ]; };
+  nativeBuildInputs = [ pkgconfig ];
+  gobject-introspection = attrs: { buildInputs = [ gtk2 pcre ]; };
 
   grpc = attrs: {
-    buildInputs = [ openssl pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ openssl ];
   };
 
   hitimes = attrs: {
@@ -166,7 +174,8 @@ in
   };
 
   pango = attrs: {
-    buildInputs = [ gtk2 xlibs.libXdmcp pcre pkgconfig xlibs.libpthreadstubs ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ gtk2 xlibs.libXdmcp pcre xlibs.libpthreadstubs ];
   };
 
   patron = attrs: {
@@ -204,7 +213,8 @@ in
   };
 
   rmagick = attrs: {
-    buildInputs = [ imagemagick pkgconfig which ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ imagemagick which ];
   };
 
   ruby-lxc = attrs: {
@@ -219,7 +229,8 @@ in
     ];
   };
   rugged = attrs: {
-    buildInputs = [ cmake pkgconfig openssl libssh2 zlib ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ cmake openssl libssh2 zlib ];
   };
 
   scrypt = attrs:
@@ -296,7 +307,8 @@ in
   xapian-ruby = attrs: {
     # use the system xapian
     dontBuild = false;
-    buildInputs = [ xapian_1_2_22 pkgconfig zlib ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ xapian_1_2_22 zlib ];
     postPatch = ''
       cp ${./xapian-Rakefile} Rakefile
     '';
diff --git a/pkgs/development/tools/analysis/kcov/default.nix b/pkgs/development/tools/analysis/kcov/default.nix
index cbe6e5fdde9e..c960f54ab204 100644
--- a/pkgs/development/tools/analysis/kcov/default.nix
+++ b/pkgs/development/tools/analysis/kcov/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   };
 
   preConfigure = "patchShebangs src/bin-to-c-source.py";
-  buildInputs = [ cmake pkgconfig zlib curl elfutils python libiberty binutils ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ cmake zlib curl elfutils python libiberty binutils ];
 
   meta = with stdenv.lib; {
     description = "Code coverage tester for compiled programs, Python scripts and shell scripts";
diff --git a/pkgs/development/tools/analysis/radare/default.nix b/pkgs/development/tools/analysis/radare/default.nix
index 6b7ba2a81cb2..31530a2751bb 100644
--- a/pkgs/development/tools/analysis/radare/default.nix
+++ b/pkgs/development/tools/analysis/radare/default.nix
@@ -21,7 +21,8 @@ stdenv.mkDerivation rec {
 
   hardeningDisable = [ "format" ];
 
-  buildInputs = [pkgconfig readline libusb perl]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ readline libusb perl]
     ++ optional useX11 [gtkdialog vte gtk2]
     ++ optional rubyBindings [ruby]
     ++ optional pythonBindings [python]
diff --git a/pkgs/development/tools/analysis/radare2/default.nix b/pkgs/development/tools/analysis/radare2/default.nix
index 1572fff40b9a..a4cf3bcd649b 100644
--- a/pkgs/development/tools/analysis/radare2/default.nix
+++ b/pkgs/development/tools/analysis/radare2/default.nix
@@ -40,7 +40,8 @@ stdenv.mkDerivation rec {
       '(*info->fprintf_func) (info->stream, "%s", errmsg);'
   '';
 
-  buildInputs = [pkgconfig readline libusb libewf perl zlib openssl]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ readline libusb libewf perl zlib openssl]
     ++ optional useX11 [gtkdialog vte gtk2]
     ++ optional rubyBindings [ruby]
     ++ optional pythonBindings [python]
diff --git a/pkgs/development/tools/analysis/smatch/default.nix b/pkgs/development/tools/analysis/smatch/default.nix
index f5c5c616979c..9dc1e2db8c09 100644
--- a/pkgs/development/tools/analysis/smatch/default.nix
+++ b/pkgs/development/tools/analysis/smatch/default.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation {
     sha256 = "0r43qi6vryqg450fj73yjwbb7gzcgx64rhrhb3r1m6a252srijiy";
   };
 
-  buildInputs = [sqlite pkgconfig perl]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [sqlite perl]
    ++ stdenv.lib.optional buildllvmsparse llvm
    ++ stdenv.lib.optional buildc2xml libxml2;
 
diff --git a/pkgs/development/tools/analysis/sparse/default.nix b/pkgs/development/tools/analysis/sparse/default.nix
index 6898b7eee54c..945f6c80af52 100644
--- a/pkgs/development/tools/analysis/sparse/default.nix
+++ b/pkgs/development/tools/analysis/sparse/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sed -i Makefile -e "s|^PREFIX=.*$|PREFIX=$out|g"
   '';
 
-  buildInputs = [ pkgconfig libxml2 llvm ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxml2 llvm ];
   doCheck = true;
 
   meta = {
diff --git a/pkgs/development/tools/build-managers/gnumake/4.2/default.nix b/pkgs/development/tools/build-managers/gnumake/4.2/default.nix
index 56d4b831460a..253aadb86d73 100644
--- a/pkgs/development/tools/build-managers/gnumake/4.2/default.nix
+++ b/pkgs/development/tools/build-managers/gnumake/4.2/default.nix
@@ -21,7 +21,8 @@ stdenv.mkDerivation {
     ./impure-dirs.patch
   ];
 
-  buildInputs = stdenv.lib.optionals guileSupport [ guile pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = stdenv.lib.optionals guileSupport [ guile ];
 
   configureFlags = stdenv.lib.optional guileSupport "--with-guile";
 
diff --git a/pkgs/development/tools/build-managers/nant/default.nix b/pkgs/development/tools/build-managers/nant/default.nix
index 858fc5b48df3..5da32f2334a7 100644
--- a/pkgs/development/tools/build-managers/nant/default.nix
+++ b/pkgs/development/tools/build-managers/nant/default.nix
@@ -15,7 +15,8 @@ let
     name = "nant-bootstrapped-${version}";
     inherit src;
 
-    buildInputs = [ pkgconfig mono makeWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ mono makeWrapper ];
 
     buildFlags = "bootstrap";
 
@@ -35,7 +36,8 @@ in stdenv.mkDerivation {
   name = "nant-${version}";
   inherit src;
 
-  buildInputs = [ pkgconfig mono makeWrapper nant-bootstrapped ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ mono makeWrapper nant-bootstrapped ];
 
   dontStrip = true;
 
diff --git a/pkgs/development/tools/build-managers/tup/default.nix b/pkgs/development/tools/build-managers/tup/default.nix
index 828fe20ecc54..fd27d927bd57 100644
--- a/pkgs/development/tools/build-managers/tup/default.nix
+++ b/pkgs/development/tools/build-managers/tup/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0jzp1llq6635ldb7j9qb29j2k0x5mblimdqg3179dvva1hv0ia23";
   };
 
-  buildInputs = [ fuse pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ fuse ];
 
   configurePhase = ''
     sed -i 's/`git describe`/v${version}/g' Tupfile
diff --git a/pkgs/development/tools/documentation/gnome-doc-utils/default.nix b/pkgs/development/tools/documentation/gnome-doc-utils/default.nix
index ef339d47ea05..5f0b6b628cb2 100644
--- a/pkgs/development/tools/documentation/gnome-doc-utils/default.nix
+++ b/pkgs/development/tools/documentation/gnome-doc-utils/default.nix
@@ -11,6 +11,7 @@ python2Packages.buildPythonApplication {
   };
 
   configureFlags = "--disable-scrollkeeper";
-  buildInputs = [ libxslt pkgconfig intltool ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxslt intltool ];
   propagatedBuildInputs = [ libxml2Python ];
 }
diff --git a/pkgs/development/tools/guile/g-wrap/default.nix b/pkgs/development/tools/guile/g-wrap/default.nix
index 030693714f07..15b552fb4aa9 100644
--- a/pkgs/development/tools/guile/g-wrap/default.nix
+++ b/pkgs/development/tools/guile/g-wrap/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
 
   # Note: Glib support is optional, but it's quite useful (e.g., it's
   # used by Guile-GNOME).
-  buildInputs = [ guile pkgconfig glib guile_lib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ guile glib guile_lib ];
 
   propagatedBuildInputs = [ libffi ];
 
diff --git a/pkgs/development/tools/libsigrok/default.nix b/pkgs/development/tools/libsigrok/default.nix
index abfbc9a6c471..1f4c21cb7f9c 100644
--- a/pkgs/development/tools/libsigrok/default.nix
+++ b/pkgs/development/tools/libsigrok/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     sha256 = "1qr02ny97navqxr56xq1a227yzf6h09m8jlvc9bnjl0bsk6887bl";
   };
 
-  buildInputs = [ pkgconfig libzip glib libusb1 libftdi1 check libserialport
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libzip glib libusb1 libftdi1 check libserialport
     librevisa doxygen glibmm python
   ];
 
diff --git a/pkgs/development/tools/libsigrokdecode/default.nix b/pkgs/development/tools/libsigrokdecode/default.nix
index e421a709c895..57bb159c5863 100644
--- a/pkgs/development/tools/libsigrokdecode/default.nix
+++ b/pkgs/development/tools/libsigrokdecode/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1hfigfj1976qk11kfsgj75l20qvyq8c9p2h4mjw23d59rsg5ga2a";
   };
 
-  buildInputs = [ pkgconfig glib python3 libsigrok check ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib python3 libsigrok check ];
 
   meta = with stdenv.lib; {
     description = "Protocol decoding library for the sigrok signal analysis software suite";
diff --git a/pkgs/development/tools/mdk/default.nix b/pkgs/development/tools/mdk/default.nix
index ca8c2de9630f..37c5dab8ce87 100644
--- a/pkgs/development/tools/mdk/default.nix
+++ b/pkgs/development/tools/mdk/default.nix
@@ -6,7 +6,8 @@ stdenv.mkDerivation {
     url = http://ftp.gnu.org/gnu/mdk/v1.2.9/mdk-1.2.9.tar.gz;
     sha256 = "0c24wzrzbk0l4z1p5nnxihaqra75amwmw59va44554infkfms9kc";
   };
-  buildInputs = [ intltool pkgconfig glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ intltool glib ];
   postInstall = ''
     mkdir -p $out/share/emacs/site-lisp/
     cp -v ./misc/*.el $out/share/emacs/site-lisp
diff --git a/pkgs/development/tools/misc/avarice/default.nix b/pkgs/development/tools/misc/avarice/default.nix
index 77cb86766692..ca6cb14c2a43 100644
--- a/pkgs/development/tools/misc/avarice/default.nix
+++ b/pkgs/development/tools/misc/avarice/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0jhh1h1k5b41v2ycq8kn43nkrkh0b9l7xjmw38rak871g3z3hix1";
   };
 
-  buildInputs = [ pkgconfig gcc perl libusb ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gcc perl libusb ];
 
   meta = {
     license = stdenv.lib.licenses.gpl2;
diff --git a/pkgs/development/tools/misc/babeltrace/default.nix b/pkgs/development/tools/misc/babeltrace/default.nix
index a82fae132552..2adc61ce6456 100644
--- a/pkgs/development/tools/misc/babeltrace/default.nix
+++ b/pkgs/development/tools/misc/babeltrace/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "0z0k4qvz4ypxs4dmgrzv9da7ylf6jr94ra6nylqpfrdspvjzwj92";
   };
 
-  buildInputs = [ pkgconfig glib libuuid popt elfutils ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib libuuid popt elfutils ];
 
   meta = with stdenv.lib; {
     description = "Command-line tool and library to read and convert LTTng tracefiles";
diff --git a/pkgs/development/tools/misc/d-feet/default.nix b/pkgs/development/tools/misc/d-feet/default.nix
index 4fec00a2fd7e..bd08c6c4c05e 100644
--- a/pkgs/development/tools/misc/d-feet/default.nix
+++ b/pkgs/development/tools/misc/d-feet/default.nix
@@ -13,7 +13,8 @@ in pythonPackages.buildPythonApplication rec {
     sha256 = "a3dc940c66f84b996c328531e3034d475ec690d7ff639445ff7ca746aa8cb9c2";
   };
 
-  buildInputs = [ pkgconfig libxml2 itstool intltool glib gtk3
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libxml2 itstool intltool glib gtk3
     gnome3.defaultIconTheme makeWrapper libwnck3
   ];
 
diff --git a/pkgs/development/tools/misc/distcc/default.nix b/pkgs/development/tools/misc/distcc/default.nix
index 17ef66470505..cef399eb5c12 100644
--- a/pkgs/development/tools/misc/distcc/default.nix
+++ b/pkgs/development/tools/misc/distcc/default.nix
@@ -16,7 +16,8 @@ let
       sha256 = "1vj31wcdas8wy52hy6749mlrca9v6ynycdiigx5ay8pnya9z73c6";
     };
 
-    buildInputs = [popt avahi pkgconfig python gtk2 autoconf automake pkgconfig which procps libiberty_static];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [popt avahi pkgconfig python gtk2 autoconf automake which procps libiberty_static];
     preConfigure =
     ''
       export CPATH=$(ls -d ${gcc.cc}/lib/gcc/*/${gcc.cc.version}/plugin/include)
diff --git a/pkgs/development/tools/misc/eggdbus/default.nix b/pkgs/development/tools/misc/eggdbus/default.nix
index a6de652f9005..27dadd08e560 100644
--- a/pkgs/development/tools/misc/eggdbus/default.nix
+++ b/pkgs/development/tools/misc/eggdbus/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "118hj63ac65zlg71kydv4607qcg1qpdlql4kvhnwnnhar421jnq4";
   };
   
-  buildInputs = [ pkgconfig glib dbus dbus_glib ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib dbus dbus_glib ];
 
   meta = {
     homepage = https://hal.freedesktop.org/releases/;
diff --git a/pkgs/development/tools/misc/fswatch/default.nix b/pkgs/development/tools/misc/fswatch/default.nix
index b8e2a9a189bc..cdddad5155ff 100644
--- a/pkgs/development/tools/misc/fswatch/default.nix
+++ b/pkgs/development/tools/misc/fswatch/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
     sha256 = "1g329aapdvbzhr39wyh295shpfq5f0nlzsqkjnr8l6zzak7f4yrg";
   };
 
-  buildInputs = [ autoreconfHook gettext libtool makeWrapper texinfo ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ gettext libtool makeWrapper texinfo ];
 
   meta = with stdenv.lib; {
     description = "A cross-platform file change monitor with multiple backends";
diff --git a/pkgs/development/tools/misc/gob2/default.nix b/pkgs/development/tools/misc/gob2/default.nix
index 4ea939b01569..ca8d0c6f7173 100644
--- a/pkgs/development/tools/misc/gob2/default.nix
+++ b/pkgs/development/tools/misc/gob2/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   };
 
   # configure script looks for d-bus but it is only needed for tests
-  buildInputs = [ glib bison flex pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib bison flex ];
 
   meta = {
     description = "Preprocessor for making GObjects with inline C code";
diff --git a/pkgs/development/tools/misc/gpshell/default.nix b/pkgs/development/tools/misc/gpshell/default.nix
index f552fe00566b..25043f89463d 100644
--- a/pkgs/development/tools/misc/gpshell/default.nix
+++ b/pkgs/development/tools/misc/gpshell/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "19a77zvyf2vazbv17185s4pynhylk2ky8vhl4i8pg9zww29sicqi";
   };
 
-  buildInputs = [ pkgconfig globalplatform pcsclite makeWrapper ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ globalplatform pcsclite makeWrapper ];
 
   postFixup = ''
     wrapProgram "$out/bin/gpshell" --prefix LD_LIBRARY_PATH : "${gppcscconnectionplugin}/lib"
diff --git a/pkgs/development/tools/misc/gtkdialog/default.nix b/pkgs/development/tools/misc/gtkdialog/default.nix
index 2641a1ed04fc..71e9ee27a9e8 100644
--- a/pkgs/development/tools/misc/gtkdialog/default.nix
+++ b/pkgs/development/tools/misc/gtkdialog/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
     sha256 = "ff89d2d7f1e6488e5df5f895716ac1d4198c2467a2a5dc1f51ab408a2faec38e";
   };
 
-  buildInputs = [ gtk2 pkgconfig hicolor_icon_theme ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gtk2 hicolor_icon_theme ];
 
   meta = {
     homepage = http://gtkdialog.googlecode.com/;
diff --git a/pkgs/development/tools/misc/kconfig-frontends/default.nix b/pkgs/development/tools/misc/kconfig-frontends/default.nix
index 8449cf9b6f38..d1415569ca33 100644
--- a/pkgs/development/tools/misc/kconfig-frontends/default.nix
+++ b/pkgs/development/tools/misc/kconfig-frontends/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     url = "http://ymorin.is-a-geek.org/download/${basename}/${name}.tar.xz";
   };
 
-  buildInputs = [ bison flex gperf ncurses pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ bison flex gperf ncurses ];
 
   hardeningDisable = [ "format" ];
 
diff --git a/pkgs/development/tools/misc/lttv/default.nix b/pkgs/development/tools/misc/lttv/default.nix
index 5cf8b6649418..45dd86db41b2 100644
--- a/pkgs/development/tools/misc/lttv/default.nix
+++ b/pkgs/development/tools/misc/lttv/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "1faldxnh9dld5k0vxckwpqw241ya1r2zv286l6rpgqr500zqw7r1";
   };
 
-  buildInputs = [ pkgconfig glib gtk2 popt babeltrace ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib gtk2 popt babeltrace ];
 
   meta = with stdenv.lib; {
     description = "Graphical trace viewer for LTTng trace files";
diff --git a/pkgs/development/tools/misc/msitools/default.nix b/pkgs/development/tools/misc/msitools/default.nix
index bdc7f4f04148..cace3e7f0a94 100644
--- a/pkgs/development/tools/misc/msitools/default.nix
+++ b/pkgs/development/tools/misc/msitools/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0bndnm3mgcqkw5dhwy5l1zri4lqvjbhbn5rxz651fkxlkhab8bhm";
   };
 
-  buildInputs = [intltool glib pkgconfig libgsf libuuid gcab bzip2];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [intltool glib libgsf libuuid gcab bzip2];
 
   meta = with stdenv.lib; {
     description = "Set of programs to inspect and build Windows Installer (.MSI) files";
diff --git a/pkgs/development/tools/misc/openocd/default.nix b/pkgs/development/tools/misc/openocd/default.nix
index 3349213a741b..2ab0dbd1b5f5 100644
--- a/pkgs/development/tools/misc/openocd/default.nix
+++ b/pkgs/development/tools/misc/openocd/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1bhn2c85rdz4gf23358kg050xlzh7yxbbwmqp24c0akmh3bff4kk";
   };
 
-  buildInputs = [ libftdi libusb1 pkgconfig hidapi ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libftdi libusb1 hidapi ];
 
   configureFlags = [
     "--enable-jtag_vpi"
diff --git a/pkgs/development/tools/misc/patchelf/unstable.nix b/pkgs/development/tools/misc/patchelf/unstable.nix
index 2443c2804435..cde8eae0f7fc 100644
--- a/pkgs/development/tools/misc/patchelf/unstable.nix
+++ b/pkgs/development/tools/misc/patchelf/unstable.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
 
   setupHook = [ ./setup-hook.sh ];
 
-  buildInputs = [ autoreconfHook ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ ];
 
   doCheck = true;
 
diff --git a/pkgs/development/tools/misc/sysbench/default.nix b/pkgs/development/tools/misc/sysbench/default.nix
index 540db210eb4e..45a31ad66f20 100644
--- a/pkgs/development/tools/misc/sysbench/default.nix
+++ b/pkgs/development/tools/misc/sysbench/default.nix
@@ -4,7 +4,8 @@
 stdenv.mkDerivation rec {
   name = "sysbench-1.0.6";
 
-  buildInputs = [ autoreconfHook pkgconfig vim libmysql libaio ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ vim libmysql libaio ];
 
   src = fetchFromGitHub {
     owner = "akopytov";
diff --git a/pkgs/development/tools/misc/universal-ctags/default.nix b/pkgs/development/tools/misc/universal-ctags/default.nix
index b0d5bcd28f79..544fc213273d 100644
--- a/pkgs/development/tools/misc/universal-ctags/default.nix
+++ b/pkgs/development/tools/misc/universal-ctags/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0nwcf5mh3ba0g23zw7ym73pgpfdass412k2fy67ryr9vnc709jkj";
   };
 
-  buildInputs = [ autoreconfHook pkgconfig ];
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ ];
 
   # remove when https://github.com/universal-ctags/ctags/pull/1267 is merged
   patches = [ ./sed-test.patch ];
diff --git a/pkgs/development/tools/parsing/hammer/default.nix b/pkgs/development/tools/parsing/hammer/default.nix
index 84e146789244..27596878f346 100644
--- a/pkgs/development/tools/parsing/hammer/default.nix
+++ b/pkgs/development/tools/parsing/hammer/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     rev = "47f34b81e4de834fd3537dd71928c4f3cdb7f533";
   };
 
-  buildInputs = [ glib pkgconfig python scons ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib python scons ];
   buildPhase = "scons prefix=$out";
   installPhase = "scons prefix=$out install";
 
diff --git a/pkgs/development/tools/profiling/oprofile/default.nix b/pkgs/development/tools/profiling/oprofile/default.nix
index ac87870eb590..dc447465b238 100644
--- a/pkgs/development/tools/profiling/oprofile/default.nix
+++ b/pkgs/development/tools/profiling/oprofile/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation rec {
       --replace "/bin/cp" "${coreutils}/bin/cp"
   '';
 
-  buildInputs = [ binutils zlib popt pkgconfig linuxHeaders libiberty_static ]
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ binutils zlib popt linuxHeaders libiberty_static ]
     ++ stdenv.lib.optionals withGUI [ qt4 ];
 
   configureFlags = [
diff --git a/pkgs/development/tools/profiling/sysprof/default.nix b/pkgs/development/tools/profiling/sysprof/default.nix
index 4be334e20ed9..001560df0a04 100644
--- a/pkgs/development/tools/profiling/sysprof/default.nix
+++ b/pkgs/development/tools/profiling/sysprof/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1wb4d844rsy8qjg3z5m6rnfm72da4xwzrrkkb1q5r10sq1pkrw5s";
   };
 
-  buildInputs = [ binutils pkgconfig gtk2 glib pango libglade ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ binutils gtk2 glib pango libglade ];
 
   meta = {
     homepage = http://sysprof.com/;
diff --git a/pkgs/development/tools/profiling/systemtap/default.nix b/pkgs/development/tools/profiling/systemtap/default.nix
index a16bdbc539a9..89a1b5fe0aac 100644
--- a/pkgs/development/tools/profiling/systemtap/default.nix
+++ b/pkgs/development/tools/profiling/systemtap/default.nix
@@ -14,7 +14,8 @@ let
   stapBuild = stdenv.mkDerivation {
     name = "systemtap-${version}";
     src = fetchgit { inherit url rev sha256; };
-    buildInputs = [ elfutils pkgconfig gettext python2 pythonPackages.setuptools ];
+  nativeBuildInputs = [ pkgconfig ];
+    buildInputs = [ elfutils gettext python2 pythonPackages.setuptools ];
     # FIXME: Workaround for bug in kbuild, where quoted -I"/foo" flags would get mangled in out-of-tree kbuild dirs
     postPatch = ''
       substituteInPlace buildrun.cxx --replace \
diff --git a/pkgs/development/tools/sigrok-cli/default.nix b/pkgs/development/tools/sigrok-cli/default.nix
index f2b7d67915a0..2d36b09adb35 100644
--- a/pkgs/development/tools/sigrok-cli/default.nix
+++ b/pkgs/development/tools/sigrok-cli/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "072ylscp0ppgii1k5j07hhv7dfmni4vyhxnsvxmgqgfyq9ldjsan";
   };
 
-  buildInputs = [ pkgconfig glib libsigrok libsigrokdecode ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ glib libsigrok libsigrokdecode ];
 
   meta = with stdenv.lib; {
     description = "Command-line frontend for the sigrok signal analysis software suite";
diff --git a/pkgs/development/tools/simavr/default.nix b/pkgs/development/tools/simavr/default.nix
index c4dd8725a1c1..e3dda5094275 100644
--- a/pkgs/development/tools/simavr/default.nix
+++ b/pkgs/development/tools/simavr/default.nix
@@ -31,7 +31,8 @@ stdenv.mkDerivation rec {
     patchelf --set-rpath "$(patchelf --print-rpath "$target"):$out/lib" "$target"
   '';
 
-  buildInputs = [ which git avrbinutils avrgcc avrlibc libelf pkgconfig freeglut mesa ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ which git avrbinutils avrgcc avrlibc libelf freeglut mesa ];
 
   meta = with stdenv.lib; {
     description = "A lean and mean Atmel AVR simulator";
diff --git a/pkgs/development/tools/skopeo/default.nix b/pkgs/development/tools/skopeo/default.nix
index 9028a796381c..a5625c225dfc 100644
--- a/pkgs/development/tools/skopeo/default.nix
+++ b/pkgs/development/tools/skopeo/default.nix
@@ -10,7 +10,8 @@ buildGoPackage rec {
   goPackagePath = "github.com/projectatomic/skopeo";
   excludedPackages = "integration";
 
-  buildInputs = [ gpgme libgpgerror devicemapper btrfs-progs pkgconfig ostree ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ gpgme libgpgerror devicemapper btrfs-progs ostree ];
 
   src = fetchFromGitHub {
     inherit rev;
diff --git a/pkgs/development/tools/sunxi-tools/default.nix b/pkgs/development/tools/sunxi-tools/default.nix
index 432560242549..59252a938637 100644
--- a/pkgs/development/tools/sunxi-tools/default.nix
+++ b/pkgs/development/tools/sunxi-tools/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation {
     sha256 = "02pqaaahra4wbv325264qh5i17mxwicmjx9nm33nw2dpmfmg9xhr";
   };
 
-  buildInputs = [ pkgconfig libusb ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libusb ];
 
   buildPhase = ''
     make all misc
diff --git a/pkgs/development/web/valum/default.nix b/pkgs/development/web/valum/default.nix
index c700fd81a245..ad11542f04b0 100644
--- a/pkgs/development/web/valum/default.nix
+++ b/pkgs/development/web/valum/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "0ca067gg5z1798bazwzgg2yd2mbysvk8i2q2v3i8d0d188y2hj84";
   };
 
-  buildInputs = [ python pkgconfig glib vala_0_28 ctpl libgee libsoup fcgi ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ python glib vala_0_28 ctpl libgee libsoup fcgi ];
 
   configurePhase = ''python waf configure --prefix=$out'';