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{ stdenv, lib, fetchFromGitHub, python, makeWrapper
, eigen, fftw, libtiff, libpng, zlib, ants, bc
, qt5, libGL, libGLU, libX11, libXext
, withGui ? true, less }:
stdenv.mkDerivation rec {
pname = "mrtrix";
version = "unstable-2021-11-25";
src = fetchFromGitHub {
owner = "MRtrix3";
repo = "mrtrix3";
rev = "994498557037c9e4f7ba67f255820ef84ea899d9";
sha256 = "sha256-8eFDS5z4ZxMzi9Khk90KAS4ndma/Syd6JDXM2Fpr0M8=";
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 >> $LOGFILE 2>&1' ""
substituteInPlace ./build \
--replace '"less -RX "' '"${less}/bin/less -RX "'
'';
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; {
broken = (stdenv.isLinux && stdenv.isAarch64);
homepage = "https://github.com/MRtrix3/mrtrix3";
description = "Suite of tools for diffusion imaging";
maintainers = with maintainers; [ bcdarwin ];
platforms = platforms.linux;
license = licenses.mpl20;
};
}
|