6 files changed, 43 insertions, 21 deletions
diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix
index 978615fa4592..7502a4ffd2ab 100644
--- a/pkgs/applications/science/biology/EZminc/default.nix
+++ b/pkgs/applications/science/biology/EZminc/default.nix
@@ -1,18 +1,18 @@
-{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk, fftwFloat, gsl }:
+{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk4, fftwFloat, gsl }:
 
 stdenv.mkDerivation rec {
   pname = "EZminc";
-  name  = "${pname}-unstable-2019-07-25";
+  name  = "${pname}-unstable-2019-03-12";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "9591edd5389a5bda2c1f606816c7cdb35c065adf";
-    sha256 = "02k87qbpx0f48l2lbcjmlqx82py684z3sfi29va5icfg3hjd6j7b";
+    rev    = "5e3333ee356f914d34d66d33ea8df809c7f7fa51";
+    sha256 = "0wy8cppf5xpgfqvgb3mqs1cjh81n6qzkk6zxv29wvng8nar9wsy4";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
-  buildInputs = [ itk libminc bicpl fftwFloat gsl ];
+  buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
 
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
                  "-DEZMINC_BUILD_TOOLS=TRUE"
diff --git a/pkgs/development/libraries/itk/default.nix b/pkgs/development/libraries/itk/default.nix
index d745ff438cee..6c0298c0f71c 100644
--- a/pkgs/development/libraries/itk/default.nix
+++ b/pkgs/development/libraries/itk/default.nix
@@ -1,14 +1,15 @@
-{ stdenv, fetchFromGitHub, cmake, libX11, libuuid, xz, vtk, darwin }:
+{ stdenv, fetchFromGitHub, cmake, makeWrapper
+, pkgconfig, libX11, libuuid, xz, vtk, Cocoa }:
 
 stdenv.mkDerivation rec {
   pname = "itk";
-  version = "5.0.1";
+  version = "5.1.0";
 
   src = fetchFromGitHub {
     owner = "InsightSoftwareConsortium";
     repo = "ITK";
     rev = "v${version}";
-    sha256 = "0dcjsn5frjnrphfgw8alnd2ahrvicpx2a2ngb5ixaa9anaicz9z1";
+    sha256 = "0rvkp00xj1js60021jv2ydyl74wvbyb205gm9d7hf8gy2q456hgl";
   };
 
   cmakeFlags = [
@@ -23,12 +24,16 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  nativeBuildInputs = [ cmake xz ];
-  buildInputs = [ libX11 libuuid vtk ] ++ stdenv.lib.optionals stdenv.isDarwin [ darwin.apple_sdk.frameworks.Cocoa ];
+  nativeBuildInputs = [ cmake xz makeWrapper ];
+  buildInputs = [ libX11 libuuid vtk ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa ];
+
+  postInstall = ''
+    wrapProgram "$out/bin/h5c++" --prefix PATH ":" "${pkgconfig}/bin"
+  '';
 
   meta = {
     description = "Insight Segmentation and Registration Toolkit";
-    homepage = "http://www.itk.org/";
+    homepage = "https://www.itk.org/";
     license = stdenv.lib.licenses.asl20;
     maintainers = with stdenv.lib.maintainers; [viric];
   };
diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix
index e5565aae29b1..4d98b12928f5 100644
--- a/pkgs/development/libraries/science/biology/elastix/default.nix
+++ b/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, itk, python3 }:
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3 }:
 
 stdenv.mkDerivation rec {
   pname    = "elastix";
@@ -11,10 +11,24 @@ stdenv.mkDerivation rec {
     sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
   };
 
+  patches = [
+    (fetchpatch {
+      name = "itk-5.1-compat.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/402e9a26f22f805b8f2db00c00e59f75fa1783ad.patch";
+      sha256 = "1il6gc1lgy78i0w6gkkppr61nh6g0yjspbfk19hcz20778m5jhz9";
+    })
+    (fetchpatch {
+      name = "fix-osx-build.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/52e1dc3928046f9fbb85d4b2ecd0d5175fa9695d.patch";
+      sha256 = "1hf7kgx1jv497pf0x5wj79sy1wncxcvhrkix9w086lcr8zwxvn9q";
+    })
+  ];
+
+
   nativeBuildInputs = [ cmake python3 ];
   buildInputs = [ itk ];
 
-  doCheck = true;
+  doCheck = !stdenv.isDarwin;  # usual dynamic linker issues
 
   preCheck = "
     export LD_LIBRARY_PATH=$(pwd)/bin
@@ -24,7 +38,7 @@ stdenv.mkDerivation rec {
     homepage = "http://elastix.isi.uu.nl/";
     description = "Image registration toolkit based on ITK";
     maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.linux;
+    platforms = platforms.x86_64;  # libitkpng linker issues with ITK 5.1
     license = licenses.asl20;
   };
 }
diff --git a/pkgs/development/libraries/simpleitk/default.nix b/pkgs/development/libraries/simpleitk/default.nix
index d6708b0dfed8..445a8bc5f21d 100644
--- a/pkgs/development/libraries/simpleitk/default.nix
+++ b/pkgs/development/libraries/simpleitk/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, git, swig, lua, itk, tcl, tk }:
+{ stdenv, fetchFromGitHub, cmake, git, swig, lua, itk4, tcl, tk }:
 
 stdenv.mkDerivation rec {
   pname = "simpleitk";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ cmake git swig ];
-  buildInputs = [ lua itk ];
+  buildInputs = [ lua itk4 ];
 
   cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_CXX_FLAGS='-Wno-attributes'" ];
 
diff --git a/pkgs/development/libraries/vtk/default.nix b/pkgs/development/libraries/vtk/default.nix
index 6a7e26c753cd..1cc706f4eb73 100644
--- a/pkgs/development/libraries/vtk/default.nix
+++ b/pkgs/development/libraries/vtk/default.nix
@@ -57,7 +57,7 @@ stdenv.mkDerivation rec {
     ++ optional enablePython [ "-DVTK_WRAP_PYTHON:BOOL=ON" ];
 
   postPatch = stdenv.lib.optionalString stdenv.isDarwin ''
-    sed -i 's|COMMAND vtkHashSource|COMMAND "DYLD_LIBRARY_PATH=''${VTK_BINARY_DIR}/lib" ''${VTK_BINARY_DIR}/bin/vtkHashSource-7.0|' ./Parallel/Core/CMakeLists.txt
+    sed -i 's|COMMAND vtkHashSource|COMMAND "DYLD_LIBRARY_PATH=''${VTK_BINARY_DIR}/lib" ''${VTK_BINARY_DIR}/bin/vtkHashSource-${majorVersion}|' ./Parallel/Core/CMakeLists.txt
     sed -i 's/fprintf(output, shift)/fprintf(output, "%s", shift)/' ./ThirdParty/libxml2/vtklibxml2/xmlschemas.c
     sed -i 's/fprintf(output, shift)/fprintf(output, "%s", shift)/g' ./ThirdParty/libxml2/vtklibxml2/xpath.c
   '';
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6a05fec52b7c..661bc75daaa4 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -12304,7 +12304,7 @@ in
   itk4 = callPackage ../development/libraries/itk/4.x.nix { stdenv = gcc8Stdenv; };
 
   itk = callPackage ../development/libraries/itk {
-    stdenv = gcc8Stdenv;
+    inherit (darwin.apple_sdk.frameworks) Cocoa;
   };
 
   jasper = callPackage ../development/libraries/jasper { };
@@ -14438,7 +14438,10 @@ in
 
   simp_le = callPackage ../tools/admin/simp_le { };
 
-  simpleitk = callPackage ../development/libraries/simpleitk { lua = lua51Packages.lua; };
+  simpleitk = callPackage ../development/libraries/simpleitk {
+    lua = lua51Packages.lua;
+    stdenv = gcc8Stdenv;
+  };
 
   sfml = callPackage ../development/libraries/sfml {
     inherit (darwin.apple_sdk.frameworks) IOKit Foundation AppKit OpenAL;
@@ -14869,7 +14872,7 @@ in
   vte_290 = callPackage ../development/libraries/vte/2.90.nix { };
 
   vtk = callPackage ../development/libraries/vtk {
-    stdenv = gcc8Stdenv;
+    stdenv = if stdenv.isDarwin then stdenv else gcc8Stdenv;
     inherit (darwin) libobjc;
     inherit (darwin.apple_sdk.libs) xpc;
     inherit (darwin.apple_sdk.frameworks) Cocoa CoreServices DiskArbitration
@@ -24354,7 +24357,7 @@ in
 
   est-sfs = callPackage ../applications/science/biology/est-sfs { };
 
-  ezminc = callPackage ../applications/science/biology/EZminc { };
+  ezminc = callPackage ../applications/science/biology/EZminc { stdenv = gcc8Stdenv; };
 
   exonerate = callPackage ../applications/science/biology/exonerate { };