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-rw-r--r--pkgs/applications/audio/MMA/default.nix3
-rw-r--r--pkgs/applications/audio/baudline/default.nix2
-rw-r--r--pkgs/applications/audio/caudec/default.nix2
-rw-r--r--pkgs/applications/audio/clementine/default.nix6
-rw-r--r--pkgs/applications/audio/clerk/default.nix3
-rw-r--r--pkgs/applications/audio/deadbeef/wrapper.nix2
-rw-r--r--pkgs/applications/audio/faust/faust1.nix7
-rw-r--r--pkgs/applications/audio/faust/faust2.nix5
-rw-r--r--pkgs/applications/audio/google-play-music-desktop-player/default.nix2
-rw-r--r--pkgs/applications/audio/jamin/default.nix4
-rw-r--r--pkgs/applications/audio/lash/default.nix4
-rw-r--r--pkgs/applications/audio/linuxband/default.nix4
-rw-r--r--pkgs/applications/audio/puredata/wrapper.nix2
-rw-r--r--pkgs/applications/audio/real_time_config_quick_scan/default.nix3
-rw-r--r--pkgs/applications/audio/rubyripper/default.nix3
-rw-r--r--pkgs/applications/audio/spotify/default.nix3
-rw-r--r--pkgs/applications/audio/vkeybd/default.nix3
-rw-r--r--pkgs/applications/editors/eclipse/default.nix2
-rw-r--r--pkgs/applications/editors/kakoune/wrapper.nix2
-rw-r--r--pkgs/applications/editors/kodestudio/default.nix3
-rw-r--r--pkgs/applications/editors/music/tuxguitar/default.nix2
-rw-r--r--pkgs/applications/editors/neovim/wrapper.nix2
-rw-r--r--pkgs/applications/editors/netbeans/default.nix3
-rw-r--r--pkgs/applications/editors/supertux-editor/default.nix4
-rw-r--r--pkgs/applications/editors/vim/macvim-configurable.nix2
-rw-r--r--pkgs/applications/editors/vscode/with-extensions.nix3
-rw-r--r--pkgs/applications/graphics/gimp/wrapper.nix2
-rw-r--r--pkgs/applications/graphics/glimpse/wrapper.nix2
-rw-r--r--pkgs/applications/graphics/imagej/default.nix3
-rw-r--r--pkgs/applications/graphics/inkscape/with-extensions.nix2
-rw-r--r--pkgs/applications/graphics/tesseract/wrapper.nix2
-rw-r--r--pkgs/applications/graphics/unigine-valley/default.nix2
-rw-r--r--pkgs/applications/misc/ape/default.nix3
-rw-r--r--pkgs/applications/misc/audio/wavesurfer/default.nix3
-rw-r--r--pkgs/applications/misc/bashSnippets/default.nix2
-rw-r--r--pkgs/applications/misc/cli-visualizer/default.nix4
-rw-r--r--pkgs/applications/misc/clipmenu/default.nix3
-rw-r--r--pkgs/applications/misc/ding/default.nix3
-rw-r--r--pkgs/applications/misc/gremlin-console/default.nix2
-rw-r--r--pkgs/applications/misc/icesl/default.nix2
-rw-r--r--pkgs/applications/misc/josm/default.nix3
-rw-r--r--pkgs/applications/misc/keepass/default.nix3
-rw-r--r--pkgs/applications/misc/mpvc/default.nix3
-rw-r--r--pkgs/applications/misc/omegat.nix3
-rw-r--r--pkgs/applications/misc/openjump/default.nix3
-rw-r--r--pkgs/applications/misc/projectlibre/default.nix3
-rw-r--r--pkgs/applications/misc/sidequest/default.nix2
-rw-r--r--pkgs/applications/misc/sweethome3d/default.nix3
-rw-r--r--pkgs/applications/misc/sweethome3d/editors.nix3
-rw-r--r--pkgs/applications/misc/tabula/default.nix2
-rw-r--r--pkgs/applications/misc/translate-shell/default.nix2
-rw-r--r--pkgs/applications/misc/viking/default.nix4
-rw-r--r--pkgs/applications/misc/wordnet/default.nix3
-rw-r--r--pkgs/applications/misc/xfontsel/default.nix4
-rw-r--r--pkgs/applications/misc/zathura/wrapper.nix3
-rw-r--r--pkgs/applications/networking/charles/default.nix2
-rw-r--r--pkgs/applications/networking/cluster/spark/default.nix3
-rw-r--r--pkgs/applications/networking/cluster/ssm-agent/default.nix2
-rw-r--r--pkgs/applications/networking/cluster/terraform/default.nix2
-rw-r--r--pkgs/applications/networking/ids/snort/default.nix3
-rw-r--r--pkgs/applications/networking/instant-messengers/gomuks/default.nix3
-rw-r--r--pkgs/applications/networking/instant-messengers/hipchat/default.nix2
-rw-r--r--pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix4
-rw-r--r--pkgs/applications/networking/instant-messengers/viber/default.nix3
-rw-r--r--pkgs/applications/networking/insync/default.nix4
-rw-r--r--pkgs/applications/networking/jnetmap/default.nix3
-rw-r--r--pkgs/applications/networking/mailreaders/evolution/evolution/wrapper.nix2
-rw-r--r--pkgs/applications/networking/p2p/vuze/default.nix3
-rw-r--r--pkgs/applications/networking/remote/vmware-horizon-client/default.nix2
-rw-r--r--pkgs/applications/networking/sync/unison/default.nix3
-rw-r--r--pkgs/applications/networking/tsung/default.nix2
-rw-r--r--pkgs/applications/networking/wg-bond/default.nix2
-rw-r--r--pkgs/applications/office/docear/default.nix3
-rw-r--r--pkgs/applications/office/impressive/default.nix3
-rw-r--r--pkgs/applications/office/treesheets/default.nix3
-rw-r--r--pkgs/applications/science/biology/eggnog-mapper/default.nix2
-rw-r--r--pkgs/applications/science/biology/platypus/default.nix3
-rw-r--r--pkgs/applications/science/biology/snpeff/default.nix3
-rw-r--r--pkgs/applications/science/biology/varscan/default.nix3
-rw-r--r--pkgs/applications/science/logic/isabelle/default.nix3
-rw-r--r--pkgs/applications/science/logic/leo2/default.nix3
-rw-r--r--pkgs/applications/science/logic/satallax/default.nix3
-rw-r--r--pkgs/applications/science/logic/tlaplus/default.nix3
-rw-r--r--pkgs/applications/science/logic/tlaplus/toolbox.nix2
-rw-r--r--pkgs/applications/science/logic/why3/with-provers.nix3
-rw-r--r--pkgs/applications/science/logic/workcraft/default.nix2
-rw-r--r--pkgs/applications/science/math/calc/default.nix3
-rw-r--r--pkgs/applications/science/math/weka/default.nix3
-rw-r--r--pkgs/applications/science/medicine/aliza/default.nix3
-rw-r--r--pkgs/applications/science/misc/cytoscape/default.nix3
-rw-r--r--pkgs/applications/science/programming/plm/default.nix3
-rw-r--r--pkgs/applications/terminal-emulators/rxvt-unicode/wrapper.nix2
-rw-r--r--pkgs/applications/terminal-emulators/terminus/default.nix3
-rw-r--r--pkgs/applications/version-management/cvs2svn/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/bfg-repo-cleaner/default.nix3
-rw-r--r--pkgs/applications/version-management/git-and-tools/fast-export/default.nix3
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-crypt/default.nix4
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-octopus/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-open/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-recent/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-reparent/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-secret/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git-sync/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/git/default.nix4
-rw-r--r--pkgs/applications/version-management/git-and-tools/gitflow/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/svn2git/default.nix2
-rw-r--r--pkgs/applications/version-management/git-and-tools/transcrypt/default.nix3
-rw-r--r--pkgs/applications/version-management/mercurial/4.9.nix3
-rw-r--r--pkgs/applications/version-management/mercurial/default.nix3
-rw-r--r--pkgs/applications/version-management/monotone-viz/default.nix4
-rw-r--r--pkgs/applications/video/lightworks/default.nix3
-rw-r--r--pkgs/applications/video/quvi/tool.nix4
-rw-r--r--pkgs/applications/video/xscast/default.nix2
-rw-r--r--pkgs/applications/virtualization/docker/gc.nix2
-rw-r--r--pkgs/applications/window-managers/leftwm/default.nix3
115 files changed, 185 insertions, 138 deletions
diff --git a/pkgs/applications/audio/MMA/default.nix b/pkgs/applications/audio/MMA/default.nix
index ade595732c3..25cb9696509 100644
--- a/pkgs/applications/audio/MMA/default.nix
+++ b/pkgs/applications/audio/MMA/default.nix
@@ -9,7 +9,8 @@
     sha256 = "18k0hwlqky5x4y461fxmw77gvz7z8jyrvxicrqphsgvwwinzy732";
   };
 
-  buildInputs = [ makeWrapper python3 alsaUtils timidity ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ python3 alsaUtils timidity ];
 
   patchPhase = ''
     sed -i 's@/usr/bin/aplaymidi@/${alsaUtils}/bin/aplaymidi@g' mma-splitrec
diff --git a/pkgs/applications/audio/baudline/default.nix b/pkgs/applications/audio/baudline/default.nix
index 29c5130f575..7d6d51011cc 100644
--- a/pkgs/applications/audio/baudline/default.nix
+++ b/pkgs/applications/audio/baudline/default.nix
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
     else
       throw "baudline isn't supported (yet?) on ${stdenv.hostPlatform.system}";
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   # Prebuilt binary distribution.
   # "patchelf --set-rpath" seems to break the application (cannot start), using
diff --git a/pkgs/applications/audio/caudec/default.nix b/pkgs/applications/audio/caudec/default.nix
index 0360922c819..15ebb85136b 100644
--- a/pkgs/applications/audio/caudec/default.nix
+++ b/pkgs/applications/audio/caudec/default.nix
@@ -17,7 +17,7 @@ stdenv.mkDerivation {
     patchShebangs ./install.sh
   '';
 
-  buildInputs = [ bash makeWrapper ];
+  nativeBuildInputs = [ bash makeWrapper ];
 
   installPhase = ''
     ./install.sh --prefix=$out/bin
diff --git a/pkgs/applications/audio/clementine/default.nix b/pkgs/applications/audio/clementine/default.nix
index be0f2f72529..e665edabd07 100644
--- a/pkgs/applications/audio/clementine/default.nix
+++ b/pkgs/applications/audio/clementine/default.nix
@@ -24,7 +24,7 @@ let
     ./clementine-spotify-blob.patch
   ];
 
-  nativeBuildInputs = [ cmake pkg-config ];
+  nativeBuildInputs = [ cmake pkg-config makeWrapper ];
 
   buildInputs = [
     boost
@@ -68,7 +68,7 @@ let
     inherit src patches nativeBuildInputs postPatch;
 
     # gst_plugins needed for setup-hooks
-    buildInputs = buildInputs ++ [ makeWrapper ] ++ gst_plugins;
+    buildInputs = buildInputs ++ gst_plugins;
 
     preConfigure = ''
       rm -rf ext/{,lib}clementine-spotifyblob
@@ -102,7 +102,7 @@ let
     # Use the same patches and sources as Clementine
     inherit src nativeBuildInputs patches postPatch;
 
-    buildInputs = buildInputs ++ [ libspotify makeWrapper ];
+    buildInputs = buildInputs ++ [ libspotify ];
     # Only build and install the Spotify blob
     preBuild = ''
       cd ext/clementine-spotifyblob
diff --git a/pkgs/applications/audio/clerk/default.nix b/pkgs/applications/audio/clerk/default.nix
index 0724632a63e..a2e71b955ec 100644
--- a/pkgs/applications/audio/clerk/default.nix
+++ b/pkgs/applications/audio/clerk/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation {
     sha256 = "0y045my65hr3hjyx13jrnyg6g3wb41phqb1m7azc4l6vx6r4124b";
   };
 
-  buildInputs = [ makeWrapper pythonPackages.mpd2 ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ pythonPackages.mpd2 ];
 
   dontBuild = true;
 
diff --git a/pkgs/applications/audio/deadbeef/wrapper.nix b/pkgs/applications/audio/deadbeef/wrapper.nix
index cd45ef5926b..66108deab1e 100644
--- a/pkgs/applications/audio/deadbeef/wrapper.nix
+++ b/pkgs/applications/audio/deadbeef/wrapper.nix
@@ -5,7 +5,7 @@ symlinkJoin {
 
   paths = [ deadbeef ] ++ plugins;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     wrapProgram $out/bin/deadbeef \
diff --git a/pkgs/applications/audio/faust/faust1.nix b/pkgs/applications/audio/faust/faust1.nix
index 6d7d2e2c2ba..81ce11b9ea1 100644
--- a/pkgs/applications/audio/faust/faust1.nix
+++ b/pkgs/applications/audio/faust/faust1.nix
@@ -30,7 +30,7 @@ let
 
     inherit src;
 
-    buildInputs = [ makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
 
     passthru = {
       inherit wrap wrapWithBuildEnv;
@@ -159,8 +159,7 @@ let
 
     stdenv.mkDerivation ((faust2ApplBase args) // {
 
-      nativeBuildInputs = [ pkg-config ];
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ pkg-config makeWrapper ];
 
       propagatedBuildInputs = [ faust ] ++ propagatedBuildInputs;
 
@@ -195,7 +194,7 @@ let
 
     in stdenv.mkDerivation ((faust2ApplBase args) // {
 
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ makeWrapper ];
 
       postFixup = ''
         for script in "$out"/bin/*; do
diff --git a/pkgs/applications/audio/faust/faust2.nix b/pkgs/applications/audio/faust/faust2.nix
index 990d073528e..051caf120fa 100644
--- a/pkgs/applications/audio/faust/faust2.nix
+++ b/pkgs/applications/audio/faust/faust2.nix
@@ -168,8 +168,7 @@ let
 
     stdenv.mkDerivation ((faust2ApplBase args) // {
 
-      nativeBuildInputs = [ pkg-config ];
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ pkg-config makeWrapper ];
 
       propagatedBuildInputs = [ faust ] ++ propagatedBuildInputs;
 
@@ -209,7 +208,7 @@ let
 
     in stdenv.mkDerivation ((faust2ApplBase args) // {
 
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ makeWrapper ];
 
       postFixup = ''
         for script in "$out"/bin/*; do
diff --git a/pkgs/applications/audio/google-play-music-desktop-player/default.nix b/pkgs/applications/audio/google-play-music-desktop-player/default.nix
index 0be1cc45717..f86eed1d34d 100644
--- a/pkgs/applications/audio/google-play-music-desktop-player/default.nix
+++ b/pkgs/applications/audio/google-play-music-desktop-player/default.nix
@@ -53,7 +53,7 @@ stdenv.mkDerivation {
   };
 
   dontBuild = true;
-  buildInputs = [ dpkg makeWrapper ];
+  nativeBuildInputs = [ dpkg makeWrapper ];
 
   unpackPhase = ''
     dpkg -x $src .
diff --git a/pkgs/applications/audio/jamin/default.nix b/pkgs/applications/audio/jamin/default.nix
index f111c4e99d7..325d115b581 100644
--- a/pkgs/applications/audio/jamin/default.nix
+++ b/pkgs/applications/audio/jamin/default.nix
@@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0g5v74cm0q3p3pzl6xmnp4rqayaymfli7c6z8s78h9rgd24fwbvn";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ fftwFloat gtk2 ladspaPlugins libjack2 liblo libxml2 makeWrapper ]
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ fftwFloat gtk2 ladspaPlugins libjack2 liblo libxml2 ]
     ++ (with perlPackages; [ perl XMLParser ]);
 
   NIX_LDFLAGS = "-ldl";
diff --git a/pkgs/applications/audio/lash/default.nix b/pkgs/applications/audio/lash/default.nix
index eb355a43409..74bbeb9b7bb 100644
--- a/pkgs/applications/audio/lash/default.nix
+++ b/pkgs/applications/audio/lash/default.nix
@@ -15,8 +15,8 @@ stdenv.mkDerivation  rec {
   # http://permalink.gmane.org/gmane.linux.redhat.fedora.extras.cvs/822346
   patches = [ ./socket.patch ./gcc-47.patch ];
 
-  buildInputs = [ alsaLib gtk2 libjack2 libxml2 makeWrapper
-    pkg-config readline ];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ alsaLib gtk2 libjack2 libxml2 readline ];
   propagatedBuildInputs = [ libuuid ];
   NIX_LDFLAGS = "-lm -lpthread -luuid";
 
diff --git a/pkgs/applications/audio/linuxband/default.nix b/pkgs/applications/audio/linuxband/default.nix
index 118b54ad858..ec034ae238d 100644
--- a/pkgs/applications/audio/linuxband/default.nix
+++ b/pkgs/applications/audio/linuxband/default.nix
@@ -11,8 +11,8 @@ in stdenv.mkDerivation rec {
     sha256 = "1r71h4yg775m4gax4irrvygmrsclgn503ykmc2qwjsxa42ri4n2n";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ makeWrapper MMA libjack2 libsmf python pyGtkGlade pygtksourceview ];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ MMA libjack2 libsmf python pyGtkGlade pygtksourceview ];
 
   patchPhase = ''
     sed -i 's@/usr/@${MMA}/@g' src/main/config/linuxband.rc.in
diff --git a/pkgs/applications/audio/puredata/wrapper.nix b/pkgs/applications/audio/puredata/wrapper.nix
index 80968e2700b..3444ef9acbd 100644
--- a/pkgs/applications/audio/puredata/wrapper.nix
+++ b/pkgs/applications/audio/puredata/wrapper.nix
@@ -7,7 +7,7 @@ in symlinkJoin {
 
   paths = [ puredata ] ++ plugins;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     wrapProgram $out/bin/pd \
diff --git a/pkgs/applications/audio/real_time_config_quick_scan/default.nix b/pkgs/applications/audio/real_time_config_quick_scan/default.nix
index 3fb476b65cc..8bc2553f521 100644
--- a/pkgs/applications/audio/real_time_config_quick_scan/default.nix
+++ b/pkgs/applications/audio/real_time_config_quick_scan/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "16kanzp5i353x972zjkwgi3m8z90wc58613mlfzb0n01djdnm6k5";
   };
 
-  buildInputs = [ perlPackages.perl makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ perlPackages.perl ];
 
   dontBuild = true;
 
diff --git a/pkgs/applications/audio/rubyripper/default.nix b/pkgs/applications/audio/rubyripper/default.nix
index b7abfa40b86..e8a275db98d 100644
--- a/pkgs/applications/audio/rubyripper/default.nix
+++ b/pkgs/applications/audio/rubyripper/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   preConfigure = "patchShebangs .";
 
   configureFlags = [ "--enable-cli" ];
-  buildInputs = [ ruby cdparanoia makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ ruby cdparanoia ];
   postInstall = ''
     wrapProgram "$out/bin/rrip_cli" \
       --prefix PATH : "${ruby}/bin" \
diff --git a/pkgs/applications/audio/spotify/default.nix b/pkgs/applications/audio/spotify/default.nix
index 43ecb67d64a..655a047a3a6 100644
--- a/pkgs/applications/audio/spotify/default.nix
+++ b/pkgs/applications/audio/spotify/default.nix
@@ -81,7 +81,8 @@ stdenv.mkDerivation {
     sha512 = "5b3d5d1f52a554c8e775b8aed16ef84e96bf3b61a2b53266e10d3c47e341899310af13cc8513b04424fc14532e36543a6fae677f80a036e3f51c75166d8d53d1";
   };
 
-  buildInputs = [ squashfsTools makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ squashfsTools ];
 
   dontStrip = true;
   dontPatchELF = true;
diff --git a/pkgs/applications/audio/vkeybd/default.nix b/pkgs/applications/audio/vkeybd/default.nix
index 3409d8a4907..943bd0d8032 100644
--- a/pkgs/applications/audio/vkeybd/default.nix
+++ b/pkgs/applications/audio/vkeybd/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation  rec {
     sha256 = "0107b5j1gf7dwp7qb4w2snj4bqiyps53d66qzl2rwj4jfpakws5a";
   };
 
-  buildInputs = [ alsaLib libX11 makeWrapper tcl tk ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ alsaLib libX11 tcl tk ];
 
   configurePhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/editors/eclipse/default.nix b/pkgs/applications/editors/eclipse/default.nix
index cff482e887d..2c067250309 100644
--- a/pkgs/applications/editors/eclipse/default.nix
+++ b/pkgs/applications/editors/eclipse/default.nix
@@ -162,7 +162,7 @@ in rec {
       # Eclipse.
       name = (lib.meta.appendToName "with-plugins" eclipse).name;
     in
-      runCommand name { buildInputs = [ makeWrapper ]; } ''
+      runCommand name { nativeBuildInputs = [ makeWrapper ]; } ''
         mkdir -p $out/bin $out/etc
 
         # Prepare an eclipse.ini with the plugin directory.
diff --git a/pkgs/applications/editors/kakoune/wrapper.nix b/pkgs/applications/editors/kakoune/wrapper.nix
index 7ac56d9cb1e..451507885ce 100644
--- a/pkgs/applications/editors/kakoune/wrapper.nix
+++ b/pkgs/applications/editors/kakoune/wrapper.nix
@@ -9,7 +9,7 @@ in
   symlinkJoin {
     name = "kakoune-${kakoune.version}";
 
-    buildInputs = [ makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
 
     paths = [ kakoune ] ++ requestedPlugins;
 
diff --git a/pkgs/applications/editors/kodestudio/default.nix b/pkgs/applications/editors/kodestudio/default.nix
index e0704cdbc85..aa7b7b19448 100644
--- a/pkgs/applications/editors/kodestudio/default.nix
+++ b/pkgs/applications/editors/kodestudio/default.nix
@@ -29,7 +29,8 @@ in
         inherit sha256;
     };
 
-    buildInputs = [ makeWrapper libXScrnSaver ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ libXScrnSaver ];
 
     desktopItem = makeDesktopItem {
       name = "kodestudio";
diff --git a/pkgs/applications/editors/music/tuxguitar/default.nix b/pkgs/applications/editors/music/tuxguitar/default.nix
index 63be87ee86c..90879b352e1 100644
--- a/pkgs/applications/editors/music/tuxguitar/default.nix
+++ b/pkgs/applications/editors/music/tuxguitar/default.nix
@@ -14,7 +14,7 @@ in stdenv.mkDerivation rec {
     sha256 = metadata.sha256;
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/editors/neovim/wrapper.nix b/pkgs/applications/editors/neovim/wrapper.nix
index 5c6c6c1a8d5..41ff62a619f 100644
--- a/pkgs/applications/editors/neovim/wrapper.nix
+++ b/pkgs/applications/editors/neovim/wrapper.nix
@@ -106,7 +106,7 @@ let
 
     preferLocalBuild = true;
 
-    buildInputs = [makeWrapper];
+    nativeBuildInputs = [ makeWrapper ];
     passthru = { unwrapped = neovim; };
 
     meta = neovim.meta // {
diff --git a/pkgs/applications/editors/netbeans/default.nix b/pkgs/applications/editors/netbeans/default.nix
index 9206b296b9a..f968b85c6ff 100644
--- a/pkgs/applications/editors/netbeans/default.nix
+++ b/pkgs/applications/editors/netbeans/default.nix
@@ -56,7 +56,8 @@ stdenv.mkDerivation {
     ln -s ${desktopItem}/share/applications/* $out/share/applications
   '';
 
-  buildInputs = [ makeWrapper perl python unzip libicns imagemagick ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ perl python unzip libicns imagemagick ];
 
   meta = {
     description = "An integrated development environment for Java, C, C++ and PHP";
diff --git a/pkgs/applications/editors/supertux-editor/default.nix b/pkgs/applications/editors/supertux-editor/default.nix
index e474ff5f19b..6e3580a563c 100644
--- a/pkgs/applications/editors/supertux-editor/default.nix
+++ b/pkgs/applications/editors/supertux-editor/default.nix
@@ -10,8 +10,8 @@ stdenv.mkDerivation {
     sha256 = "08y5haclgxvcii3hpdvn1ah8qd0f3n8xgxxs8zryj02b8n7cz3vx";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [mono gtk-sharp-2_0 makeWrapper gnome2.libglade gtk2 ];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [mono gtk-sharp-2_0 gnome2.libglade gtk2 ];
 
   installPhase = ''
     mkdir -p $out/bin $out/lib/supertux-editor
diff --git a/pkgs/applications/editors/vim/macvim-configurable.nix b/pkgs/applications/editors/vim/macvim-configurable.nix
index 6ea6b6c6094..7ed3dee9b6b 100644
--- a/pkgs/applications/editors/vim/macvim-configurable.nix
+++ b/pkgs/applications/editors/vim/macvim-configurable.nix
@@ -29,7 +29,7 @@ let
           "/Applications/MacVim.app/Contents/MacOS"
           "/Applications/MacVim.app/Contents/bin"
         ];
-        buildInputs = [ makeWrapper ];
+        nativeBuildInputs = [ makeWrapper ];
         # We need to do surgery on the resulting app. We can't just make a wrapper for vim because this
         # is a GUI app. We need to copy the actual GUI executable image as AppKit uses the loaded image's
         # path to locate the bundle. We can use symlinks for other executables and resources though.
diff --git a/pkgs/applications/editors/vscode/with-extensions.nix b/pkgs/applications/editors/vscode/with-extensions.nix
index c30b52782ef..d2c91f155d5 100644
--- a/pkgs/applications/editors/vscode/with-extensions.nix
+++ b/pkgs/applications/editors/vscode/with-extensions.nix
@@ -57,7 +57,8 @@ in
 # When no extensions are requested, we simply redirect to the original
 # non-wrapped vscode executable.
 runCommand "${wrappedPkgName}-with-extensions-${wrappedPkgVersion}" {
-  buildInputs = [ vscode makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ vscode ];
   dontPatchELF = true;
   dontStrip = true;
   meta = vscode.meta;
diff --git a/pkgs/applications/graphics/gimp/wrapper.nix b/pkgs/applications/graphics/gimp/wrapper.nix
index 8fde04d0d1d..bb81a374fea 100644
--- a/pkgs/applications/graphics/gimp/wrapper.nix
+++ b/pkgs/applications/graphics/gimp/wrapper.nix
@@ -11,7 +11,7 @@ in symlinkJoin {
 
   paths = [ gimp ] ++ selectedPlugins;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     for each in gimp-${versionBranch} gimp-console-${versionBranch}; do
diff --git a/pkgs/applications/graphics/glimpse/wrapper.nix b/pkgs/applications/graphics/glimpse/wrapper.nix
index cdfb2f66873..daa540d31e5 100644
--- a/pkgs/applications/graphics/glimpse/wrapper.nix
+++ b/pkgs/applications/graphics/glimpse/wrapper.nix
@@ -12,7 +12,7 @@ symlinkJoin {
 
   paths = [ glimpse ] ++ selectedPlugins;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     for each in glimpse-${versionBranch} glimpse-console-${versionBranch}; do
diff --git a/pkgs/applications/graphics/imagej/default.nix b/pkgs/applications/graphics/imagej/default.nix
index 7e3238e94bb..312316b3397 100644
--- a/pkgs/applications/graphics/imagej/default.nix
+++ b/pkgs/applications/graphics/imagej/default.nix
@@ -15,7 +15,8 @@ let
       url = "https://wsr.imagej.net/distros/cross-platform/ij150.zip";
       sha256 = "97aba6fc5eb908f5160243aebcdc4965726693cb1353d9c0d71b8f5dd832cb7b";
     };
-    buildInputs = [ unzip makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ unzip ];
     inherit jre;
 
     # JAR files that are intended to be used by other packages
diff --git a/pkgs/applications/graphics/inkscape/with-extensions.nix b/pkgs/applications/graphics/inkscape/with-extensions.nix
index cca7b1fc3a5..c558a6bb062 100644
--- a/pkgs/applications/graphics/inkscape/with-extensions.nix
+++ b/pkgs/applications/graphics/inkscape/with-extensions.nix
@@ -10,7 +10,7 @@ symlinkJoin {
 
   paths = [ inkscape ] ++ inkscapeExtensions;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     rm -f $out/bin/inkscape
diff --git a/pkgs/applications/graphics/tesseract/wrapper.nix b/pkgs/applications/graphics/tesseract/wrapper.nix
index 313920d8154..1dfc4393c46 100644
--- a/pkgs/applications/graphics/tesseract/wrapper.nix
+++ b/pkgs/applications/graphics/tesseract/wrapper.nix
@@ -17,7 +17,7 @@ let
   tesseractWithData = tesseractBase.overrideAttrs (_: {
     inherit tesseractBase tessdata;
 
-    buildInputs = [ makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
 
     buildCommand = ''
       makeWrapper {$tesseractBase,$out}/bin/tesseract --set-default TESSDATA_PREFIX $out/share/tessdata
diff --git a/pkgs/applications/graphics/unigine-valley/default.nix b/pkgs/applications/graphics/unigine-valley/default.nix
index 0c5c8f3ff28..3187f573de7 100644
--- a/pkgs/applications/graphics/unigine-valley/default.nix
+++ b/pkgs/applications/graphics/unigine-valley/default.nix
@@ -38,7 +38,7 @@ in
     sourceRoot = "Unigine_Valley-${version}";
     instPath = "lib/unigine/valley";
 
-    buildInputs = [file makeWrapper];
+    nativeBuildInputs = [file makeWrapper];
 
     libPath = lib.makeLibraryPath [
       stdenv.cc.cc  # libstdc++.so.6
diff --git a/pkgs/applications/misc/ape/default.nix b/pkgs/applications/misc/ape/default.nix
index f16d6e15733..c359d606a85 100644
--- a/pkgs/applications/misc/ape/default.nix
+++ b/pkgs/applications/misc/ape/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   inherit pname;
   version = "2019-08-10";
 
-  buildInputs = [ swiProlog makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ swiProlog ];
 
   src = fetchFromGitHub {
      owner = "Attempto";
diff --git a/pkgs/applications/misc/audio/wavesurfer/default.nix b/pkgs/applications/misc/audio/wavesurfer/default.nix
index 6e276d592b0..b7e738cfc12 100644
--- a/pkgs/applications/misc/audio/wavesurfer/default.nix
+++ b/pkgs/applications/misc/audio/wavesurfer/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation {
     sha256 = "1yx9s1j47cq0v40cwq2gn7bdizpw46l95ba4zl9z4gg31mfvm807";
   };
 
-  buildInputs = [ snack tcl tk makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ snack tcl tk ];
 
   installPhase = ''
     mkdir -p $out/{bin,nix-support,share/wavesurfer/}
diff --git a/pkgs/applications/misc/bashSnippets/default.nix b/pkgs/applications/misc/bashSnippets/default.nix
index 4a023849f39..d50f3637988 100644
--- a/pkgs/applications/misc/bashSnippets/default.nix
+++ b/pkgs/applications/misc/bashSnippets/default.nix
@@ -22,7 +22,7 @@ stdenv.mkDerivation {
     sha256 = "044nxgd3ic2qr6hgq5nymn3dyf5i4s8mv5z4az6jvwlrjnvbg8cp";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   patchPhase = ''
     patchShebangs install.sh
diff --git a/pkgs/applications/misc/cli-visualizer/default.nix b/pkgs/applications/misc/cli-visualizer/default.nix
index 74dd82a3c6e..524f8985537 100644
--- a/pkgs/applications/misc/cli-visualizer/default.nix
+++ b/pkgs/applications/misc/cli-visualizer/default.nix
@@ -15,9 +15,9 @@ stdenv.mkDerivation rec {
     sed '1i#include <cmath>' -i src/Transformer/SpectrumCircleTransformer.cpp
   '';
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake makeWrapper ];
 
-  buildInputs = [ fftw ncurses5 libpulseaudio makeWrapper ];
+  buildInputs = [ fftw ncurses5 libpulseaudio ];
 
   buildFlags = [ "ENABLE_PULSE=1" ];
 
diff --git a/pkgs/applications/misc/clipmenu/default.nix b/pkgs/applications/misc/clipmenu/default.nix
index e3a0046205e..c47dd972ccf 100644
--- a/pkgs/applications/misc/clipmenu/default.nix
+++ b/pkgs/applications/misc/clipmenu/default.nix
@@ -27,8 +27,7 @@ stdenv.mkDerivation rec {
   '';
 
   makeFlags = [ "PREFIX=$(out)" ];
-  buildInputs = [ makeWrapper ];
-  nativeBuildInputs = [ xsel clipnotify ];
+  nativeBuildInputs = [ makeWrapper xsel clipnotify ];
 
   postFixup = ''
     sed -i "$out/bin/clipctl" -e 's,clipmenud\$,\.clipmenud-wrapped\$,'
diff --git a/pkgs/applications/misc/ding/default.nix b/pkgs/applications/misc/ding/default.nix
index 36e2923522d..649fbe55fae 100644
--- a/pkgs/applications/misc/ding/default.nix
+++ b/pkgs/applications/misc/ding/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-aabIH894WihsBTo1LzIBzIZxxyhRYVxLcHpDQwmwmOU=";
   };
 
-  buildInputs = [ aspellEnv fortune gnugrep makeWrapper tk tre ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ aspellEnv fortune gnugrep tk tre ];
 
   patches = [ ./dict.patch ];
 
diff --git a/pkgs/applications/misc/gremlin-console/default.nix b/pkgs/applications/misc/gremlin-console/default.nix
index 6c3ba132d0b..22444e22054 100644
--- a/pkgs/applications/misc/gremlin-console/default.nix
+++ b/pkgs/applications/misc/gremlin-console/default.nix
@@ -8,7 +8,7 @@ stdenv.mkDerivation rec {
     sha256 = "13ycr6ppyrz9rq7dasabjdk8lcsxdj3krb4j7d2jmbh2hij1rdvf";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     mkdir -p $out/opt
diff --git a/pkgs/applications/misc/icesl/default.nix b/pkgs/applications/misc/icesl/default.nix
index 9f1431a2340..5c50ac24538 100644
--- a/pkgs/applications/misc/icesl/default.nix
+++ b/pkgs/applications/misc/icesl/default.nix
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     sha256 = "0sl54fsb2gz6dy0bwdscpdq1ab6ph5b7zald3bwzgkqsvna7p1jr";
   } else throw "Unsupported architecture";
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
   installPhase = ''
     cp -r ./ $out
     mkdir $out/oldbin
diff --git a/pkgs/applications/misc/josm/default.nix b/pkgs/applications/misc/josm/default.nix
index 28c7de12c8c..3828fc654d6 100644
--- a/pkgs/applications/misc/josm/default.nix
+++ b/pkgs/applications/misc/josm/default.nix
@@ -23,7 +23,8 @@ stdenv.mkDerivation {
 
   dontUnpack = true;
 
-  buildInputs = lib.optionals (!stdenv.isDarwin) [ jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = lib.optionals (!stdenv.isDarwin) [ jre ];
 
   installPhase =
     if stdenv.isDarwin then ''
diff --git a/pkgs/applications/misc/keepass/default.nix b/pkgs/applications/misc/keepass/default.nix
index 32572ffcdb3..6388d005fe5 100644
--- a/pkgs/applications/misc/keepass/default.nix
+++ b/pkgs/applications/misc/keepass/default.nix
@@ -12,7 +12,8 @@ with builtins; buildDotnetPackage rec {
 
   sourceRoot = ".";
 
-  buildInputs = [ unzip makeWrapper icoutils ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ unzip icoutils ];
 
   patches = [
     (substituteAll {
diff --git a/pkgs/applications/misc/mpvc/default.nix b/pkgs/applications/misc/mpvc/default.nix
index 64b55cce7a0..69aca239d31 100644
--- a/pkgs/applications/misc/mpvc/default.nix
+++ b/pkgs/applications/misc/mpvc/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation {
     wrapProgram $out/bin/mpvc --prefix PATH : "${socat}/bin/"
   '';
 
-  buildInputs = [ socat makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ socat ];
 
   meta = with lib; {
     description = "A mpc-like control interface for mpv";
diff --git a/pkgs/applications/misc/omegat.nix b/pkgs/applications/misc/omegat.nix
index 7b91d245f81..2bb3d14e1d2 100644
--- a/pkgs/applications/misc/omegat.nix
+++ b/pkgs/applications/misc/omegat.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation {
     sha256 = "0axz7r30p34z5hgvdglznc82g7yvm3g56dv5190jixskx6ba58rs";
   };
 
-  buildInputs = [ unzip makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ unzip ];
 
   unpackCmd = "unzip -o $curSrc";  # tries to go interactive without -o
 
diff --git a/pkgs/applications/misc/openjump/default.nix b/pkgs/applications/misc/openjump/default.nix
index 28becefa5b1..b3e93ce5127 100644
--- a/pkgs/applications/misc/openjump/default.nix
+++ b/pkgs/applications/misc/openjump/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation {
     cd $out; unzip $src
   '';
 
-  buildInputs = [unzip makeWrapper];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ unzip ];
 
   installPhase = ''
     dir=$(echo $out/OpenJUMP-*)
diff --git a/pkgs/applications/misc/projectlibre/default.nix b/pkgs/applications/misc/projectlibre/default.nix
index fd83d74edd5..ceb61d71866 100644
--- a/pkgs/applications/misc/projectlibre/default.nix
+++ b/pkgs/applications/misc/projectlibre/default.nix
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "0vy5vgbp45ai957gaby2dj1hvmbxfdlfnwcanwqm9f8q16qipdbq";
   };
 
-  buildInputs = [ ant jdk makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ ant jdk ];
   buildPhase = ''
     export ANT_OPTS=-Dbuild.sysclasspath=ignore
     ${ant}/bin/ant -f openproj_build/build.xml
diff --git a/pkgs/applications/misc/sidequest/default.nix b/pkgs/applications/misc/sidequest/default.nix
index 6dad2eaf812..c904c221260 100644
--- a/pkgs/applications/misc/sidequest/default.nix
+++ b/pkgs/applications/misc/sidequest/default.nix
@@ -19,7 +19,7 @@
         sha256 = "0fw952kdh1gn00y6sx2ag0rnb2paxq9ikg4bzgmbj7rrd1c6l2k9";
       };
 
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ makeWrapper ];
 
       buildCommand = ''
         mkdir -p "$out/lib/SideQuest" "$out/bin"
diff --git a/pkgs/applications/misc/sweethome3d/default.nix b/pkgs/applications/misc/sweethome3d/default.nix
index afbf5b364ed..e1be229b087 100644
--- a/pkgs/applications/misc/sweethome3d/default.nix
+++ b/pkgs/applications/misc/sweethome3d/default.nix
@@ -34,7 +34,8 @@ let
       patchelf --set-rpath ${libXxf86vm}/lib lib/java3d-1.6/linux/i586/libnativewindow_x11.so
     '';
 
-    buildInputs = [ ant jdk makeWrapper p7zip gtk3 gsettings-desktop-schemas ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ ant jdk p7zip gtk3 gsettings-desktop-schemas ];
 
     buildPhase = ''
       ant furniture textures help
diff --git a/pkgs/applications/misc/sweethome3d/editors.nix b/pkgs/applications/misc/sweethome3d/editors.nix
index 08bc5b90fd9..c0cdc764dc3 100644
--- a/pkgs/applications/misc/sweethome3d/editors.nix
+++ b/pkgs/applications/misc/sweethome3d/editors.nix
@@ -23,7 +23,8 @@ let
       categories = "Graphics;2DGraphics;3DGraphics;";
     };
 
-    buildInputs = [ ant jre jdk makeWrapper gtk3 gsettings-desktop-schemas ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ ant jre jdk gtk3 gsettings-desktop-schemas ];
 
     patchPhase = ''
       sed -i -e 's,../SweetHome3D,${application.src},g' build.xml
diff --git a/pkgs/applications/misc/tabula/default.nix b/pkgs/applications/misc/tabula/default.nix
index 1804f3c04e8..b396c578c90 100644
--- a/pkgs/applications/misc/tabula/default.nix
+++ b/pkgs/applications/misc/tabula/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   };
 
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
 
   installPhase = ''
diff --git a/pkgs/applications/misc/translate-shell/default.nix b/pkgs/applications/misc/translate-shell/default.nix
index 03ed031be85..319ba3643da 100644
--- a/pkgs/applications/misc/translate-shell/default.nix
+++ b/pkgs/applications/misc/translate-shell/default.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "075vqnha21rhr1b61dim7dqlfwm1yffyzcaa83s36rpk9r5sddzx";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installFlags = [ "PREFIX=$(out)" ];
 
diff --git a/pkgs/applications/misc/viking/default.nix b/pkgs/applications/misc/viking/default.nix
index 61ebfb0fcc6..71f67baa6c5 100644
--- a/pkgs/applications/misc/viking/default.nix
+++ b/pkgs/applications/misc/viking/default.nix
@@ -25,8 +25,8 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ makeWrapper intltool gettext gtk2 expat curl gpsd bc file gnome-doc-utils
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ intltool gettext gtk2 expat curl gpsd bc file gnome-doc-utils
     libexif libxml2 libxslt scrollkeeper docbook_xml_dtd_412 gexiv2
   ] ++ lib.optional withMapnik mapnik
     ++ lib.optional withGeoClue geoclue2
diff --git a/pkgs/applications/misc/wordnet/default.nix b/pkgs/applications/misc/wordnet/default.nix
index 32c1f0eaa64..27694174d70 100644
--- a/pkgs/applications/misc/wordnet/default.nix
+++ b/pkgs/applications/misc/wordnet/default.nix
@@ -8,7 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "08pgjvd2vvmqk3h641x63nxp7wqimb9r30889mkyfh2agc62sjbc";
   };
 
-  buildInputs = [ tcl tk xlibsWrapper makeWrapper ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ tcl tk xlibsWrapper ]
     ++ lib.optionals stdenv.isDarwin [ Cocoa ];
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/applications/misc/xfontsel/default.nix b/pkgs/applications/misc/xfontsel/default.nix
index 10034fbe1b1..365f6217861 100644
--- a/pkgs/applications/misc/xfontsel/default.nix
+++ b/pkgs/applications/misc/xfontsel/default.nix
@@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0700lf6hx7dg88wq1yll7zjvf9gbwh06xff20yffkxb289y0pai5";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [libX11 makeWrapper libXaw];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [libX11 libXaw];
 
   # Without this, it gets Xmu as a dependency, but without rpath entry
   NIX_LDFLAGS = "-lXmu";
diff --git a/pkgs/applications/misc/zathura/wrapper.nix b/pkgs/applications/misc/zathura/wrapper.nix
index 60e3bb9fd53..49f78729a31 100644
--- a/pkgs/applications/misc/zathura/wrapper.nix
+++ b/pkgs/applications/misc/zathura/wrapper.nix
@@ -4,8 +4,7 @@ symlinkJoin {
 
   paths = with zathura_core; [ man dev out ] ++ plugins;
 
-
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = let
     fishCompletion = "share/fish/vendor_completions.d/zathura.fish";
diff --git a/pkgs/applications/networking/charles/default.nix b/pkgs/applications/networking/charles/default.nix
index 03d1911333e..1dd0b408a13 100644
--- a/pkgs/applications/networking/charles/default.nix
+++ b/pkgs/applications/networking/charles/default.nix
@@ -28,7 +28,7 @@ let
         url = "https://www.charlesproxy.com/assets/release/${version}/charles-proxy-${version}.tar.gz";
         inherit sha256;
       };
-      buildInputs = [ makeWrapper ];
+      nativeBuildInputs = [ makeWrapper ];
 
       installPhase = ''
         makeWrapper ${jdk8.jre}/bin/java $out/bin/charles \
diff --git a/pkgs/applications/networking/cluster/spark/default.nix b/pkgs/applications/networking/cluster/spark/default.nix
index 071636ec443..76230b8e100 100644
--- a/pkgs/applications/networking/cluster/spark/default.nix
+++ b/pkgs/applications/networking/cluster/spark/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
     sha256 = "1a9w5k0207fysgpxx6db3a00fs5hdc2ncx99x4ccy2s0v5ndc66g";
   };
 
-  buildInputs = [ makeWrapper jre pythonPackages.python pythonPackages.numpy ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre pythonPackages.python pythonPackages.numpy ]
     ++ optional RSupport R;
 
   untarDir = "${pname}-${version}-bin-without-hadoop";
diff --git a/pkgs/applications/networking/cluster/ssm-agent/default.nix b/pkgs/applications/networking/cluster/ssm-agent/default.nix
index 928fb351c6a..b042f8ff15f 100644
--- a/pkgs/applications/networking/cluster/ssm-agent/default.nix
+++ b/pkgs/applications/networking/cluster/ssm-agent/default.nix
@@ -14,7 +14,7 @@ buildGoPackage rec {
     "agent/cli-main"
   ];
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   src = fetchFromGitHub {
     rev    = version;
diff --git a/pkgs/applications/networking/cluster/terraform/default.nix b/pkgs/applications/networking/cluster/terraform/default.nix
index 59a7039fb28..4a6e95057a4 100644
--- a/pkgs/applications/networking/cluster/terraform/default.nix
+++ b/pkgs/applications/networking/cluster/terraform/default.nix
@@ -117,7 +117,7 @@ let
         else
           lib.appendToName "with-plugins" (stdenv.mkDerivation {
             inherit (terraform) name meta;
-            buildInputs = [ makeWrapper ];
+            nativeBuildInputs = [ makeWrapper ];
 
             buildCommand = pluginDir + ''
               mkdir -p $out/bin/
diff --git a/pkgs/applications/networking/ids/snort/default.nix b/pkgs/applications/networking/ids/snort/default.nix
index 17ace3021d8..714ca1c8990 100644
--- a/pkgs/applications/networking/ids/snort/default.nix
+++ b/pkgs/applications/networking/ids/snort/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "13lzvjli6kbsnkd7lf0rm71l2mnz38pxk76ia9yrjb6clfhlbb73";
   };
 
-  buildInputs = [ makeWrapper pkg-config luajit openssl libpcap pcre libdnet daq zlib flex bison libtirpc ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ pkg-config luajit openssl libpcap pcre libdnet daq zlib flex bison libtirpc ];
 
   NIX_CFLAGS_COMPILE = [ "-I${libtirpc.dev}/include/tirpc" ];
 
diff --git a/pkgs/applications/networking/instant-messengers/gomuks/default.nix b/pkgs/applications/networking/instant-messengers/gomuks/default.nix
index a2d12124dbf..428e4e70601 100644
--- a/pkgs/applications/networking/instant-messengers/gomuks/default.nix
+++ b/pkgs/applications/networking/instant-messengers/gomuks/default.nix
@@ -26,7 +26,8 @@ buildGoModule rec {
 
   doCheck = false;
 
-  buildInputs = [ makeWrapper olm ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ olm ];
 
   # Upstream issue: https://github.com/tulir/gomuks/issues/260
   patches = lib.optional stdenv.isLinux (substituteAll {
diff --git a/pkgs/applications/networking/instant-messengers/hipchat/default.nix b/pkgs/applications/networking/instant-messengers/hipchat/default.nix
index f3736bfc64f..cbbe74481c2 100644
--- a/pkgs/applications/networking/instant-messengers/hipchat/default.nix
+++ b/pkgs/applications/networking/instant-messengers/hipchat/default.nix
@@ -47,7 +47,7 @@ in stdenv.mkDerivation {
     sha256 = "03pz8wskafn848yvciq29kwdvqcgjrk6sjnm8nk9acl89xf0sn96";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   buildCommand = ''
     ar x $src
diff --git a/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix b/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
index bc66d77e224..041ec5e7c5b 100644
--- a/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
@@ -9,8 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1argdzbif1vdmwp5vqbgkadq9ancjmgdm2ncp0qfckni715ss4rh";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ glib telepathy-glib dbus-glib libxslt telepathy-glib.python (lib.getLib dconf) makeWrapper ];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ glib telepathy-glib dbus-glib libxslt telepathy-glib.python (lib.getLib dconf) ];
 
   preFixup = ''
     wrapProgram "$out/libexec/telepathy-idle" \
diff --git a/pkgs/applications/networking/instant-messengers/viber/default.nix b/pkgs/applications/networking/instant-messengers/viber/default.nix
index 4389ee153c5..0224edc652f 100644
--- a/pkgs/applications/networking/instant-messengers/viber/default.nix
+++ b/pkgs/applications/networking/instant-messengers/viber/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation {
     sha256 = "0rs26x0lycavybn6k1hbb5kzms0zzcmxlrmi4g8k7vyafj6s8dqh";
   };
 
-  buildInputs = [ dpkg makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ dpkg ];
 
   dontUnpack = true;
 
diff --git a/pkgs/applications/networking/insync/default.nix b/pkgs/applications/networking/insync/default.nix
index b52a81932e4..380aad6c329 100644
--- a/pkgs/applications/networking/insync/default.nix
+++ b/pkgs/applications/networking/insync/default.nix
@@ -12,9 +12,7 @@ stdenv.mkDerivation rec {
     else
       throw "${pname}-${version} is not supported on ${stdenv.hostPlatform.system}";
 
-  buildInputs = [ makeWrapper ];
-
-  nativeBuildInputs = [ autoPatchelfHook ];
+  nativeBuildInputs = [ makeWrapper autoPatchelfHook ];
 
   postPatch = ''
     patchelf --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" client/insync-portable
diff --git a/pkgs/applications/networking/jnetmap/default.nix b/pkgs/applications/networking/jnetmap/default.nix
index bac0048cc28..e6332832e3e 100644
--- a/pkgs/applications/networking/jnetmap/default.nix
+++ b/pkgs/applications/networking/jnetmap/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0nxsfa600jhazwbabxmr9j37mhwysp0fyrvczhv3f1smiy8rjanl";
   };
 
-  buildInputs = [ jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
 
   dontUnpack = true;
 
diff --git a/pkgs/applications/networking/mailreaders/evolution/evolution/wrapper.nix b/pkgs/applications/networking/mailreaders/evolution/evolution/wrapper.nix
index 050082c6f93..ea3f09b8f4c 100644
--- a/pkgs/applications/networking/mailreaders/evolution/evolution/wrapper.nix
+++ b/pkgs/applications/networking/mailreaders/evolution/evolution/wrapper.nix
@@ -4,7 +4,7 @@ symlinkJoin {
   name = "evolution-with-plugins";
   paths = [ gnome3.evolution-data-server ] ++ plugins;
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   postBuild = ''
     for i in $out/bin/* $out/libexec/**; do
diff --git a/pkgs/applications/networking/p2p/vuze/default.nix b/pkgs/applications/networking/p2p/vuze/default.nix
index 557914439a9..fe8743ee1cd 100644
--- a/pkgs/applications/networking/p2p/vuze/default.nix
+++ b/pkgs/applications/networking/p2p/vuze/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "07w6ipyiy8hi88d6yxbbf3vkv26mj7dcz9yr8141hb2ig03v0h0p";
   };
 
-  buildInputs = [ makeWrapper jdk ant ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jdk ant ];
 
   buildPhase = "ant";
 
diff --git a/pkgs/applications/networking/remote/vmware-horizon-client/default.nix b/pkgs/applications/networking/remote/vmware-horizon-client/default.nix
index a9ddf48bae6..f52373f2624 100644
--- a/pkgs/applications/networking/remote/vmware-horizon-client/default.nix
+++ b/pkgs/applications/networking/remote/vmware-horizon-client/default.nix
@@ -52,7 +52,7 @@ let
       url = "https://download3.vmware.com/software/view/viewclients/CART21FQ4/VMware-Horizon-Client-Linux-2012-8.1.0-17349998.tar.gz";
       sha256 = "0afda1f3116e75a4e7f89990d8ee60ccea5f3bb8a2360652162fa11c795724ce";
     };
-    buildInputs = [ makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
     installPhase = ''
       mkdir ext $out
       find ${sysArch} -type f -print0 | xargs -0n1 tar -Cext --strip-components=1 -xf
diff --git a/pkgs/applications/networking/sync/unison/default.nix b/pkgs/applications/networking/sync/unison/default.nix
index 86126e86169..23bbd19b00e 100644
--- a/pkgs/applications/networking/sync/unison/default.nix
+++ b/pkgs/applications/networking/sync/unison/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation (rec {
     sha256 = "sha256-42hmdMwOYSWGiDCmhuqtpCWtvtyD2l+kA/bhHD/Qh5Y=";
   };
 
-  buildInputs = [ ocaml makeWrapper ncurses ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ ocaml ncurses ];
 
   preBuild = (if enableX11 then ''
     sed -i "s|\(OCAMLOPT=.*\)$|\1 -I $(echo "${lablgtk}"/lib/ocaml/*/site-lib/lablgtk2)|" src/Makefile.OCaml
diff --git a/pkgs/applications/networking/tsung/default.nix b/pkgs/applications/networking/tsung/default.nix
index 41bc6c64da8..346fd175257 100644
--- a/pkgs/applications/networking/tsung/default.nix
+++ b/pkgs/applications/networking/tsung/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     sha256 = "6394445860ef34faedf8c46da95a3cb206bc17301145bc920151107ffa2ce52a";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
   propagatedBuildInputs = [
     erlang
     gnuplot
diff --git a/pkgs/applications/networking/wg-bond/default.nix b/pkgs/applications/networking/wg-bond/default.nix
index 32ffbde400b..bef44d42862 100644
--- a/pkgs/applications/networking/wg-bond/default.nix
+++ b/pkgs/applications/networking/wg-bond/default.nix
@@ -12,7 +12,7 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "1v2az0v6l8mqryvq3898hm7bpvqdd2c4kpv6ck7932jfjyna512k";
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
   postInstall = ''
     wrapProgram $out/bin/wg-bond --set PATH ${
       lib.makeBinPath [ wireguard-tools ]
diff --git a/pkgs/applications/office/docear/default.nix b/pkgs/applications/office/docear/default.nix
index 683e6681573..f8cd25ad784 100644
--- a/pkgs/applications/office/docear/default.nix
+++ b/pkgs/applications/office/docear/default.nix
@@ -12,7 +12,8 @@ stdenv.mkDerivation {
     sha256 = "1g5n7r2x4gas6dl2fbyh7v9yxdcb6bzml8n3ldmpzv1rncgjcdp4";
   };
 
-  buildInputs = [ oraclejre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ oraclejre ];
 
   buildPhase = "";
   installPhase = ''
diff --git a/pkgs/applications/office/impressive/default.nix b/pkgs/applications/office/impressive/default.nix
index 4614a543694..f46d893d894 100644
--- a/pkgs/applications/office/impressive/default.nix
+++ b/pkgs/applications/office/impressive/default.nix
@@ -16,7 +16,8 @@ in stdenv.mkDerivation {
       sha256 = "1r7ihv41awnlnlry1kymb8fka053wdhzibfwcarn78rr3vs338vl";
     };
 
-    buildInputs = [ makeWrapper pythonEnv ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ pythonEnv ];
 
     configurePhase = ''
       # Let's fail at build time if the library we're substituting in doesn't
diff --git a/pkgs/applications/office/treesheets/default.nix b/pkgs/applications/office/treesheets/default.nix
index 552d28d1e95..1f084e182af 100644
--- a/pkgs/applications/office/treesheets/default.nix
+++ b/pkgs/applications/office/treesheets/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0krsj7i5yr76imf83krz2lmlmpbsvpwqg2d4r0jwxiydjfyj4qr4";
   };
 
-  buildInputs = [ wxGTK makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ wxGTK ];
 
   preConfigure = "cd src";
 
diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix
index 7eb3afd437a..b42fed8da28 100644
--- a/pkgs/applications/science/biology/eggnog-mapper/default.nix
+++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -16,7 +16,7 @@ python27Packages.buildPythonApplication rec {
     sha256 = "0abnmn0bh11jihf5d3cggiild1ykawzv5f5fhb4cyyi8fvy4hcxf";
   });
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
   propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ];
 
   # make emapper find diamond & hmmer
diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix
index 30bc68fb0e8..d602395b875 100644
--- a/pkgs/applications/science/biology/platypus/default.nix
+++ b/pkgs/applications/science/biology/platypus/default.nix
@@ -13,7 +13,8 @@ in stdenv.mkDerivation {
     sha256 = "0nah6r54b8xm778gqyb8b7rsd76z8ji4g73sm6rvpw5s96iib1vw";
   };
 
-  buildInputs = [ htslib python zlib makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ htslib python zlib ];
 
   buildPhase = ''
     patchShebangs .
diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix
index 32701af8392..b48e13ecf00 100644
--- a/pkgs/applications/science/biology/snpeff/default.nix
+++ b/pkgs/applications/science/biology/snpeff/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm";
   };
 
-  buildInputs = [ unzip jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ unzip jre ];
 
   sourceRoot = "snpEff";
 
diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix
index 65a19b83a70..2a232d64693 100644
--- a/pkgs/applications/science/biology/varscan/default.nix
+++ b/pkgs/applications/science/biology/varscan/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-+yO3KrZ2+1qJvQIJHCtsmv8hC5a+4E2d7mrvTYtygU0=";
   };
 
-  buildInputs = [ jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
 
   phases = [ "installPhase" ];
 
diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index a0f81a543f1..600ae83ff91 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
       sha256 = "1bibabhlsvf6qsjjkgxcpq3cvl1z7r8yfcgqbhbvsiv69n3gyfk3";
     };
 
-  buildInputs = [ perl polyml z3 makeWrapper ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ perl polyml z3 ]
              ++ lib.optionals (!stdenv.isDarwin) [ nettools java ];
 
   sourceRoot = dirname;
diff --git a/pkgs/applications/science/logic/leo2/default.nix b/pkgs/applications/science/logic/leo2/default.nix
index 520c47d7500..fc2c1e5cba4 100644
--- a/pkgs/applications/science/logic/leo2/default.nix
+++ b/pkgs/applications/science/logic/leo2/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1wjpmizb181iygnd18lx7p77fwaci2clgzs5ix5j51cc8f3pazmv";
   };
 
-  buildInputs = [ makeWrapper eprover ocaml perl zlib ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ eprover ocaml perl zlib ];
 
   sourceRoot = "leo2/src";
 
diff --git a/pkgs/applications/science/logic/satallax/default.nix b/pkgs/applications/science/logic/satallax/default.nix
index dffb66b2fcf..8c88f47327e 100644
--- a/pkgs/applications/science/logic/satallax/default.nix
+++ b/pkgs/applications/science/logic/satallax/default.nix
@@ -3,7 +3,8 @@ stdenv.mkDerivation rec {
   pname = "satallax";
   version = "2.7";
 
-  buildInputs = [ocaml zlib which eprover makeWrapper coq];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ocaml zlib which eprover coq];
   src = fetchurl {
     url = "https://www.ps.uni-saarland.de/~cebrown/satallax/downloads/${pname}-${version}.tar.gz";
     sha256 = "1kvxn8mc35igk4vigi5cp7w3wpxk2z3bgwllfm4n3h2jfs0vkpib";
diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix
index c4ba334b85f..f002b808e0a 100644
--- a/pkgs/applications/science/logic/tlaplus/default.nix
+++ b/pkgs/applications/science/logic/tlaplus/default.nix
@@ -13,7 +13,8 @@ stdenv.mkDerivation rec {
     sha256 = "1mm6r9bq79zks50yk0agcpdkw9yy994m38ibmgpb3bi3wkpq9891";
   };
 
-  buildInputs = [ makeWrapper adoptopenjdk-bin ant ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ adoptopenjdk-bin ant ];
 
   buildPhase = "ant -f tlatools/org.lamport.tlatools/customBuild.xml compile dist";
   installPhase = ''
diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix
index 1c33d923289..da8985818e7 100644
--- a/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix
@@ -28,7 +28,7 @@ in stdenv.mkDerivation {
     sha256 = "0v15wscawair5bghr5ixb4i062kmh9by1m0hnz2r1sawlqyafz02";
   };
 
-  buildInputs = [ makeWrapper  ];
+  nativeBuildInputs = [ makeWrapper ];
 
   phases = [ "installPhase" ];
 
diff --git a/pkgs/applications/science/logic/why3/with-provers.nix b/pkgs/applications/science/logic/why3/with-provers.nix
index 3528dbd3a64..d4fdbfd6937 100644
--- a/pkgs/applications/science/logic/why3/with-provers.nix
+++ b/pkgs/applications/science/logic/why3/with-provers.nix
@@ -15,7 +15,8 @@ in stdenv.mkDerivation {
 
   phases = [ "buildPhase" "installPhase" ];
 
-  buildInputs = [ why3 makeWrapper ] ++ provers;
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ why3 ] ++ provers;
 
   buildPhase = ''
       mkdir -p $out/share/why3/
diff --git a/pkgs/applications/science/logic/workcraft/default.nix b/pkgs/applications/science/logic/workcraft/default.nix
index cb0d668f536..7fb73419c07 100644
--- a/pkgs/applications/science/logic/workcraft/default.nix
+++ b/pkgs/applications/science/logic/workcraft/default.nix
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "0v71x3fph2j3xrnysvkm7zsgnbxisfbdfgxzvzxxfdg59a6l3xid";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
 
diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix
index c5449171fff..9c5a8960d32 100644
--- a/pkgs/applications/science/math/calc/default.nix
+++ b/pkgs/applications/science/math/calc/default.nix
@@ -19,7 +19,8 @@ stdenv.mkDerivation rec {
       --replace '-install_name ''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}'
   '';
 
-  buildInputs = [ util-linux makeWrapper ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ util-linux ]
              ++ lib.optionals enableReadline [ readline ncurses ];
 
   makeFlags = [
diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix
index 179801da379..05b95140b1b 100644
--- a/pkgs/applications/science/math/weka/default.nix
+++ b/pkgs/applications/science/math/weka/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0zwmhspmqb0a7cm6k6i0s6q3w19ws1g9dx3cp2v3g3vsif6cdh31";
   };
 
-  buildInputs = [ unzip makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ unzip ];
 
   # The -Xmx1000M comes suggested from their download page:
   # http://www.cs.waikato.ac.nz/ml/weka/downloading.html
diff --git a/pkgs/applications/science/medicine/aliza/default.nix b/pkgs/applications/science/medicine/aliza/default.nix
index c6bfd6361f2..e8e764ef26d 100644
--- a/pkgs/applications/science/medicine/aliza/default.nix
+++ b/pkgs/applications/science/medicine/aliza/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation {
     name = "aliza.rpm";
   };
 
-  buildInputs = [ rpmextract makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ rpmextract ];
 
   unpackCmd = "rpmextract $curSrc";
 
diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix
index db98e0db348..3ab7d57f95a 100644
--- a/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/pkgs/applications/science/misc/cytoscape/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  buildInputs = [jre makeWrapper];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
 
   installPhase = ''
     mkdir -pv $out/{share,bin}
diff --git a/pkgs/applications/science/programming/plm/default.nix b/pkgs/applications/science/programming/plm/default.nix
index dd61c3668cc..e56282b6863 100644
--- a/pkgs/applications/science/programming/plm/default.nix
+++ b/pkgs/applications/science/programming/plm/default.nix
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec {
     name = "${pname}-${version}.jar";
   };
 
-  buildInputs = [ makeWrapper jre gcc valgrind ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre gcc valgrind ];
 
   phases = [ "installPhase" ];
 
diff --git a/pkgs/applications/terminal-emulators/rxvt-unicode/wrapper.nix b/pkgs/applications/terminal-emulators/rxvt-unicode/wrapper.nix
index b03acb99530..5255d40b9ce 100644
--- a/pkgs/applications/terminal-emulators/rxvt-unicode/wrapper.nix
+++ b/pkgs/applications/terminal-emulators/rxvt-unicode/wrapper.nix
@@ -40,7 +40,7 @@ let
 
         paths = [ rxvt-unicode-unwrapped ] ++ plugins ++ extraDeps;
 
-        buildInputs = [ makeWrapper ];
+        nativeBuildInputs = [ makeWrapper ];
 
         postBuild = ''
           wrapProgram $out/bin/urxvt \
diff --git a/pkgs/applications/terminal-emulators/terminus/default.nix b/pkgs/applications/terminal-emulators/terminus/default.nix
index 67c660275f5..87394241ef7 100644
--- a/pkgs/applications/terminal-emulators/terminus/default.nix
+++ b/pkgs/applications/terminal-emulators/terminus/default.nix
@@ -18,7 +18,8 @@ stdenv.mkDerivation rec {
     url = "https://github.com/Eugeny/terminus/releases/download/v${version}/terminus_${version}_amd64.deb";
     sha256 = "1r5n75n71zwahg4rxlnf9qzrb0651gxv0987m6bykqmfpnw91nmb";
   };
-  buildInputs = [ dpkg makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ dpkg ];
   unpackPhase = ''
     mkdir pkg
     dpkg-deb -x $src pkg
diff --git a/pkgs/applications/version-management/cvs2svn/default.nix b/pkgs/applications/version-management/cvs2svn/default.nix
index ae1929565b6..af2b5cdc9a3 100644
--- a/pkgs/applications/version-management/cvs2svn/default.nix
+++ b/pkgs/applications/version-management/cvs2svn/default.nix
@@ -12,7 +12,7 @@ python2Packages.buildPythonApplication  rec {
     sha256 = "1ska0z15sjhyfi860rjazz9ya1gxbf5c0h8dfqwz88h7fccd22b4";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   checkInputs = [ subversion git breezy ];
 
diff --git a/pkgs/applications/version-management/git-and-tools/bfg-repo-cleaner/default.nix b/pkgs/applications/version-management/git-and-tools/bfg-repo-cleaner/default.nix
index 1ffc0653675..036eef1c9c3 100644
--- a/pkgs/applications/version-management/git-and-tools/bfg-repo-cleaner/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/bfg-repo-cleaner/default.nix
@@ -15,7 +15,8 @@ in
       sha256 = "1kn84rsvms1v5l1j2xgrk7dc7mnsmxkc6sqd94mnim22vnwvl8mz";
     };
 
-    buildInputs = [ jre makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ jre ];
 
     phases = "installPhase";
 
diff --git a/pkgs/applications/version-management/git-and-tools/fast-export/default.nix b/pkgs/applications/version-management/git-and-tools/fast-export/default.nix
index 5aea15769c0..565fe180ba1 100644
--- a/pkgs/applications/version-management/git-and-tools/fast-export/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/fast-export/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "0hzyh66rlawxip4n2pvz7pbs0cq82clqv1d6c7hf60v1drjxw287";
   };
 
-  buildInputs = [mercurial.python mercurial makeWrapper];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [mercurial.python mercurial];
 
   installPhase = ''
     binPath=$out/bin
diff --git a/pkgs/applications/version-management/git-and-tools/git-crypt/default.nix b/pkgs/applications/version-management/git-and-tools/git-crypt/default.nix
index 08875dabd0f..f0184c66377 100644
--- a/pkgs/applications/version-management/git-and-tools/git-crypt/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-crypt/default.nix
@@ -13,9 +13,9 @@ stdenv.mkDerivation rec {
     sha256 = "13m9y0m6gc3mlw3pqv9x4i0him2ycbysizigdvdanhh514kga602";
   };
 
-  nativeBuildInputs = [ libxslt ];
+  nativeBuildInputs = [ libxslt makeWrapper ];
 
-  buildInputs = [ openssl makeWrapper ];
+  buildInputs = [ openssl ];
 
   patchPhase = ''
     substituteInPlace commands.cpp \
diff --git a/pkgs/applications/version-management/git-and-tools/git-octopus/default.nix b/pkgs/applications/version-management/git-and-tools/git-octopus/default.nix
index 942a12e239b..7b8b5fed90f 100644
--- a/pkgs/applications/version-management/git-and-tools/git-octopus/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-octopus/default.nix
@@ -8,7 +8,7 @@ stdenv.mkDerivation rec {
 
   installFlags = [ "prefix=$(out)" ];
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   # perl provides shasum
   postInstall = ''
diff --git a/pkgs/applications/version-management/git-and-tools/git-open/default.nix b/pkgs/applications/version-management/git-and-tools/git-open/default.nix
index 5e5bba3df72..c67a575172c 100644
--- a/pkgs/applications/version-management/git-and-tools/git-open/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-open/default.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "11n46bngvca5wbdbfcxzjhjbfdbad7sgf7h9gf956cb1q8swsdm0";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   buildPhase = null;
 
diff --git a/pkgs/applications/version-management/git-and-tools/git-recent/default.nix b/pkgs/applications/version-management/git-and-tools/git-recent/default.nix
index 2ecc5d872b8..1a1811b2f43 100644
--- a/pkgs/applications/version-management/git-and-tools/git-recent/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-recent/default.nix
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     sha256 = "1g8i6vpjnnfh7vc1269c91bap267w4bxdqqwnzb8x18vqgn2fx8i";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   buildPhase = null;
 
diff --git a/pkgs/applications/version-management/git-and-tools/git-reparent/default.nix b/pkgs/applications/version-management/git-and-tools/git-reparent/default.nix
index 037de14658d..ec1c44b9613 100644
--- a/pkgs/applications/version-management/git-and-tools/git-reparent/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-reparent/default.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "0v0yxydpw6r4awy0hb7sbnh520zsk86ibzh1xjf3983yhsvkfk5v";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   dontBuild = true;
 
diff --git a/pkgs/applications/version-management/git-and-tools/git-secret/default.nix b/pkgs/applications/version-management/git-and-tools/git-secret/default.nix
index eea7bed011b..3143d7ef9c3 100644
--- a/pkgs/applications/version-management/git-and-tools/git-secret/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-secret/default.nix
@@ -14,7 +14,7 @@ in stdenv.mkDerivation {
     sha256 = "0hc7yavcp8jmn6b7wngjqhy8kl7f4191sfpik8ycvqghkvvimxj4";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     install -D git-secret $out/bin/git-secret
diff --git a/pkgs/applications/version-management/git-and-tools/git-sync/default.nix b/pkgs/applications/version-management/git-and-tools/git-sync/default.nix
index 87cb7452c75..add7bfc5526 100644
--- a/pkgs/applications/version-management/git-and-tools/git-sync/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-sync/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     sha256 = "01if8y93wa0mwbkzkzx2v1vqh47zlz4k1dysl6yh5rmppd1psknz";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   dontBuild = true;
 
diff --git a/pkgs/applications/version-management/git-and-tools/git/default.nix b/pkgs/applications/version-management/git-and-tools/git/default.nix
index 8761fc9fbca..c955c04d779 100644
--- a/pkgs/applications/version-management/git-and-tools/git/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git/default.nix
@@ -67,10 +67,10 @@ stdenv.mkDerivation {
         --subst-var-by gettext ${gettext}
   '';
 
-  nativeBuildInputs = [ gettext perlPackages.perl ]
+  nativeBuildInputs = [ gettext perlPackages.perl makeWrapper ]
     ++ lib.optionals withManual [ asciidoctor texinfo xmlto docbook2x
          docbook_xsl docbook_xsl_ns docbook_xml_dtd_45 libxslt ];
-  buildInputs = [curl openssl zlib expat cpio makeWrapper libiconv]
+  buildInputs = [curl openssl zlib expat cpio libiconv]
     ++ lib.optionals perlSupport [ perlPackages.perl ]
     ++ lib.optionals guiSupport [tcl tk]
     ++ lib.optionals withpcre2 [ pcre2 ]
diff --git a/pkgs/applications/version-management/git-and-tools/gitflow/default.nix b/pkgs/applications/version-management/git-and-tools/gitflow/default.nix
index 08bf5eb6ba0..6572b9b7fc8 100644
--- a/pkgs/applications/version-management/git-and-tools/gitflow/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/gitflow/default.nix
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-kHirHG/bfsU6tKyQ0khNSTyChhzHfzib+HyA3LOtBI8=";
   };
 
-  buildInputs = [ pkgs.makeWrapper ];
+  nativeBuildInputs = [ pkgs.makeWrapper ];
 
   preBuild = ''
     makeFlagsArray+=(prefix="$out")
diff --git a/pkgs/applications/version-management/git-and-tools/svn2git/default.nix b/pkgs/applications/version-management/git-and-tools/svn2git/default.nix
index 69742b6d760..74f10a14288 100644
--- a/pkgs/applications/version-management/git-and-tools/svn2git/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/svn2git/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation {
     sha256 = "0ly2vrv6q31n0xhciwb7a1ilr5c6ndyi3bg81yfp4axiypps7l41";
   };
 
-  buildInputs = [ ruby makeWrapper ];
+  nativeBuildInputs = [ ruby makeWrapper ];
 
   dontBuild = true;
 
diff --git a/pkgs/applications/version-management/git-and-tools/transcrypt/default.nix b/pkgs/applications/version-management/git-and-tools/transcrypt/default.nix
index aebd488fe30..3225744abc5 100644
--- a/pkgs/applications/version-management/git-and-tools/transcrypt/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/transcrypt/default.nix
@@ -11,7 +11,8 @@ stdenv.mkDerivation rec {
     sha256 = "1dkr69plk16wllk5bzlkchrzw63pk239dgbjhrb3mb61i065jdam";
   };
 
-  buildInputs = [ makeWrapper git openssl coreutils util-linux gnugrep gnused gawk ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ git openssl coreutils util-linux gnugrep gnused gawk ];
 
   patches = [ ./helper-scripts_depspathprefix.patch ];
 
diff --git a/pkgs/applications/version-management/mercurial/4.9.nix b/pkgs/applications/version-management/mercurial/4.9.nix
index 29440724274..f499be17f7c 100644
--- a/pkgs/applications/version-management/mercurial/4.9.nix
+++ b/pkgs/applications/version-management/mercurial/4.9.nix
@@ -21,7 +21,8 @@ in python2Packages.buildPythonApplication {
 
   inherit python; # pass it so that the same version can be used in hg2git
 
-  buildInputs = [ makeWrapper docutils unzip ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ docutils unzip ]
     ++ lib.optionals stdenv.isDarwin [ ApplicationServices ];
 
   propagatedBuildInputs = [ hg-git dulwich ];
diff --git a/pkgs/applications/version-management/mercurial/default.nix b/pkgs/applications/version-management/mercurial/default.nix
index c841482126a..7c0a96583e7 100644
--- a/pkgs/applications/version-management/mercurial/default.nix
+++ b/pkgs/applications/version-management/mercurial/default.nix
@@ -19,7 +19,8 @@ in python3Packages.buildPythonApplication rec {
 
   passthru = { inherit python; }; # pass it so that the same version can be used in hg2git
 
-  buildInputs = [ makeWrapper docutils unzip ]
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ docutils unzip ]
     ++ lib.optionals stdenv.isDarwin [ ApplicationServices ];
 
   makeFlags = [ "PREFIX=$(out)" ];
diff --git a/pkgs/applications/version-management/monotone-viz/default.nix b/pkgs/applications/version-management/monotone-viz/default.nix
index d6d55eaa4eb..56cc2a4ea5a 100644
--- a/pkgs/applications/version-management/monotone-viz/default.nix
+++ b/pkgs/applications/version-management/monotone-viz/default.nix
@@ -13,8 +13,8 @@ stdenv.mkDerivation rec {
   version = "1.0.2";
   pname = "monotone-viz";
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ocaml lablgtk libgnomecanvas glib graphviz_2_0 makeWrapper camlp4];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ocaml lablgtk libgnomecanvas glib graphviz_2_0 camlp4];
   src = fetchurl {
     url = "http://oandrieu.nerim.net/monotone-viz/${pname}-${version}-nolablgtk.tar.gz";
     sha256 = "1l5x4xqz5g1aaqbc1x80mg0yzkiah9ma9k9mivmn08alkjlakkdk";
diff --git a/pkgs/applications/video/lightworks/default.nix b/pkgs/applications/video/lightworks/default.nix
index 1776aab0033..0312c34bf70 100644
--- a/pkgs/applications/video/lightworks/default.nix
+++ b/pkgs/applications/video/lightworks/default.nix
@@ -30,7 +30,8 @@ let
         }
       else throw "${pname}-${version} is not supported on ${stdenv.hostPlatform.system}";
 
-    buildInputs = [ dpkg makeWrapper ];
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ dpkg ];
 
     phases = [ "unpackPhase" "installPhase" ];
     unpackPhase = "dpkg-deb -x ${src} ./";
diff --git a/pkgs/applications/video/quvi/tool.nix b/pkgs/applications/video/quvi/tool.nix
index 6718fc1dc36..87c8066a976 100644
--- a/pkgs/applications/video/quvi/tool.nix
+++ b/pkgs/applications/video/quvi/tool.nix
@@ -9,8 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "1h52s265rp3af16dvq1xlscp2926jqap2l4ah94vrfchv6m1hffb";
   };
 
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ lua5 curl quvi_scripts libquvi glib makeWrapper ];
+  nativeBuildInputs = [ pkg-config makeWrapper ];
+  buildInputs = [ lua5 curl quvi_scripts libquvi glib ];
   postInstall = ''
       wrapProgram $out/bin/quvi --set LUA_PATH "${lua5_sockets}/share/lua/${lua5.luaversion}/?.lua"
   '';
diff --git a/pkgs/applications/video/xscast/default.nix b/pkgs/applications/video/xscast/default.nix
index 49f5b43bb73..6501a399088 100644
--- a/pkgs/applications/video/xscast/default.nix
+++ b/pkgs/applications/video/xscast/default.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation {
     sha256 = "0br27bq9bpglfdpv63h827bipgvhlh10liyhmhcxls4227kagz72";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     runHook preInstall
diff --git a/pkgs/applications/virtualization/docker/gc.nix b/pkgs/applications/virtualization/docker/gc.nix
index f7bd5a4b069..52ca54501d7 100644
--- a/pkgs/applications/virtualization/docker/gc.nix
+++ b/pkgs/applications/virtualization/docker/gc.nix
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     sha256 = "07wf9yn0f771xkm3x12946x5rp83hxjkd70xgfgy35zvj27wskzm";
   };
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/window-managers/leftwm/default.nix b/pkgs/applications/window-managers/leftwm/default.nix
index 72170401d79..04c232a3e89 100644
--- a/pkgs/applications/window-managers/leftwm/default.nix
+++ b/pkgs/applications/window-managers/leftwm/default.nix
@@ -17,7 +17,8 @@ rustPlatform.buildRustPackage rec {
 
   cargoSha256 = "sha256-j57LHPU3U3ipUGQDrZ8KCuELOVJ3BxhLXsJePOO6rTM=";
 
-  buildInputs = [ makeWrapper libX11 libXinerama ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ libX11 libXinerama ];
 
   postInstall = ''
     wrapProgram $out/bin/leftwm --prefix LD_LIBRARY_PATH : "${rpath}"