1 files changed, 92 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
new file mode 100644
index 000000000000..e0b122778d1b
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
@@ -0,0 +1,92 @@
+{ stdenv, lib, fetchFromGitHub, python, makeWrapper
+, eigen, fftw, libtiff, libpng, zlib, ants, bc
+, qt5, libGL, libGLU, libX11, libXext
+, withGui ? true }:
+
+stdenv.mkDerivation rec {
+  pname = "mrtrix";
+  version = "3.0.2";
+
+  src = fetchFromGitHub {
+    owner  = "MRtrix3";
+    repo   = "mrtrix3";
+    rev    = version;
+    sha256 = "0p4d1230j6664rnb9l65cpyfj9ncbcm39yv1r9y77br9rkkv1za3";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [ eigen makeWrapper ] ++ lib.optional withGui qt5.wrapQtAppsHook;
+
+  buildInputs = [
+    ants
+    python
+    fftw
+    libtiff
+    libpng
+    zlib
+  ] ++ lib.optionals withGui [
+    libGL
+    libGLU
+    libX11
+    libXext
+    qt5.qtbase
+    qt5.qtsvg
+  ];
+
+  installCheckInputs = [ bc ];
+
+  postPatch = ''
+    patchShebangs ./build ./configure ./run_tests ./bin/*
+
+    # patching interpreters before fixup is needed for tests:
+    patchShebangs ./bin/*
+    patchShebangs testing/binaries/data/vectorstats/*py
+
+    substituteInPlace ./run_tests  \
+      --replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""
+  '';
+
+  configurePhase = ''
+    export EIGEN_CFLAGS="-isystem ${eigen}/include/eigen3"
+    unset LD  # similar to https://github.com/MRtrix3/mrtrix3/issues/1519
+    ./configure ${lib.optionalString (!withGui) "-nogui"};
+  '';
+
+  buildPhase = ''
+    ./build
+    (cd testing && ../build)
+  '';
+
+  installCheckPhase = ''
+    ./run_tests units
+    ./run_tests binaries
+
+    # can also `./run_tests scripts`, but this fails due to lack of FSL package
+    # (and there's no convenient way to disable individual tests)
+  '';
+  doInstallCheck = true;
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out
+    cp -ar lib $out/lib
+    cp -ar bin $out/bin
+    runHook postInstall
+  '';
+
+  postInstall = ''
+    for prog in $out/bin/*; do
+      if [[ -x "$prog" ]]; then
+        wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+      fi
+    done
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/MRtrix3/mrtrix3";
+    description = "Suite of tools for diffusion imaging";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license   = licenses.mpl20;
+  };
+}