From 6aa3deeb50e2f96c62cde67d86336dc631a76f57 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Thu, 15 Nov 2018 17:20:24 -0500
Subject: [PATCH 1/2] niftyreg: init at 1.3.9

---
 .../science/biology/niftyreg/default.nix      | 24 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 26 insertions(+)
 create mode 100644 pkgs/applications/science/biology/niftyreg/default.nix

diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix
new file mode 100644
index 00000000000..9f24046b3bf
--- /dev/null
+++ b/pkgs/applications/science/biology/niftyreg/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, lib, fetchurl, cmake, zlib }:
+
+stdenv.mkDerivation rec {
+  pname   = "niftyreg";
+  version = "1.3.9";
+  name    = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/${pname}/nifty_reg-${version}/nifty_reg-${version}.tar.gz";
+    sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib ];
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg;
+    description = "Medical image registration software";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = [ "x86_64-linux" ];
+    license   = licenses.bsd3;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 476d3be9093..84d6af1aacb 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21194,6 +21194,8 @@ with pkgs;
 
   ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { };
 
+  niftyreg = callPackage ../applications/science/biology/niftyreg { };
+
   paml = callPackage ../applications/science/biology/paml { };
 
   picard-tools = callPackage ../applications/science/biology/picard-tools { };

From cb6d819b9339bc0854110d13a18a6c64f89ea4ad Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Thu, 15 Nov 2018 17:34:57 -0500
Subject: [PATCH 2/2] niftyseg: init at 1.0.0

---
 .../science/biology/niftyseg/default.nix      | 24 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 26 insertions(+)
 create mode 100644 pkgs/applications/science/biology/niftyseg/default.nix

diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix
new file mode 100644
index 00000000000..671ee4b95c6
--- /dev/null
+++ b/pkgs/applications/science/biology/niftyseg/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, lib, fetchurl, cmake, eigen, zlib }:
+
+stdenv.mkDerivation rec {
+  pname   = "niftyseg";
+  version = "1.0";
+  name = "${pname}-${version}";
+  src = fetchurl {
+    url    = "https://github.com/KCL-BMEIS/NiftySeg/archive/v${version}.tar.gz";
+    sha256 = "11q6yldsxp3k6gfp94c0xhcan2y3finzv8lzizmrc79yps3wjkn0";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ eigen zlib ];
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = http://cmictig.cs.ucl.ac.uk/research/software/software-nifty/niftyseg;
+    description = "Software for medical image segmentation, bias field correction, and cortical thickness calculation";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license   = licenses.bsd3;
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 84d6af1aacb..4522fb4fdd3 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21196,6 +21196,8 @@ with pkgs;
 
   niftyreg = callPackage ../applications/science/biology/niftyreg { };
 
+  niftyseg = callPackage ../applications/science/biology/niftyseg { };
+
   paml = callPackage ../applications/science/biology/paml { };
 
   picard-tools = callPackage ../applications/science/biology/picard-tools { };