mrtrix: init at 3.0_RC3_latest

This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.

Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
This commit is contained in:
Ben Darwin 2020-02-16 14:45:22 -05:00
parent 591fca255e
commit 9a2cd20478
2 changed files with 79 additions and 0 deletions

@ -0,0 +1,77 @@
{ stdenv, lib, fetchFromGitHub, python, makeWrapper
, eigen, fftw, libtiff, zlib, ants, bc
, qt5, libGL, libGLU, libX11, libXext
, withGui ? true }:
stdenv.mkDerivation rec {
pname = "mrtrix";
version = "3.0_RC3_latest";
src = fetchFromGitHub {
owner = "MRtrix3";
repo = "mrtrix3";
rev = version;
sha256 = "184nv524p8j94qicjy9l288bqcgl2yxqqs55a7042i0gfsnwp51c";
fetchSubmodules = true;
};
nativeBuildInputs = [ eigen makeWrapper ] ++ lib.optional withGui qt5.wrapQtAppsHook;
buildInputs = [
ants
python
fftw
libtiff
zlib ] ++ lib.optionals withGui [
libGL
libGLU
libX11
libXext
qt5.qtbase
qt5.qtsvg
];
installCheckInputs = [ bc ];
postPatch = ''
patchShebangs ./build ./configure ./run_tests ./bin/population_template
substituteInPlace ./run_tests \
--replace 'git submodule update --init >> $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";
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
wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
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;
};
}

@ -23907,6 +23907,8 @@ in
mrbayes = callPackage ../applications/science/biology/mrbayes { };
mrtrix = callPackage ../applications/science/biology/mrtrix { python = python3; };
megahit = callPackage ../applications/science/biology/megahit { };
messer-slim = callPackage ../applications/science/biology/messer-slim { };