pyrox.dev
mrtrix: 3.0.4 -> 3.0.4-unstable-2025-04-09 (#397641)
authored by
Peder Bergebakken Sundt
and committed by
GitHub
2d2805b3
3a7dc008
+68
-16
pkgs/applications/science/biology/mrtrix/default.nix
+68
-16
pkgs/applications/science/biology/mrtrix/default.nix
···
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libXext,
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less,
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withGui ? true,
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fetchFromGitLab,
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fetchpatch,
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}:
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let
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# reverts 'eigen: 3.4.0 -> 3.4.0-unstable-2022-05-19'
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# https://github.com/NixOS/nixpkgs/commit/d298f046edabc84b56bd788e11eaf7ed72f8171c
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eigen' = (
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eigen.overrideAttrs (old: rec {
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version = "3.4.0";
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src = fetchFromGitLab {
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owner = "libeigen";
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repo = "eigen";
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tag = version;
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hash = "sha256-1/4xMetKMDOgZgzz3WMxfHUEpmdAm52RqZvz6i0mLEw=";
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};
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patches = (old.patches or [ ]) ++ [
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# Fixes e.g. onnxruntime on aarch64-darwin:
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# https://hydra.nixos.org/build/248915128/nixlog/1,
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# originally suggested in https://github.com/NixOS/nixpkgs/pull/258392.
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#
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# The patch is from
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# ["Fix vectorized reductions for Eigen::half"](https://gitlab.com/libeigen/eigen/-/merge_requests/699)
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# which is two years old,
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# but Eigen hasn't had a release in two years either:
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# https://gitlab.com/libeigen/eigen/-/issues/2699.
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(fetchpatch {
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url = "https://gitlab.com/libeigen/eigen/-/commit/d0e3791b1a0e2db9edd5f1d1befdb2ac5a40efe0.patch";
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hash = "sha256-8qiNpuYehnoiGiqy0c3Mcb45pwrmc6W4rzCxoLDSvj0=";
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})
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];
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})
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);
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in
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stdenv.mkDerivation rec {
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pname = "mrtrix";
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version = "3.0.4";
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version = "3.0.4-unstable-2025-04-09";
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src = fetchFromGitHub {
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owner = "MRtrix3";
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repo = "mrtrix3";
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tag = version;
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hash = "sha256-87zBAoBLWQPccGS37XyQ8H0GhL01k8GQFgcLL6IwbcM=";
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rev = "7843bfc53a75f465901804ccf3fd6797d77531dd";
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hash = "sha256-C4Io3VkX10eWia4djrYvN12fWmwm0j1G60I8lmFH49w=";
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fetchSubmodules = true;
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};
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nativeBuildInputs = [
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eigen
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makeWrapper
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less
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python
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] ++ lib.optional withGui qt5.wrapQtAppsHook;
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buildInputs =
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[
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ants
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eigen'
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python
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fftw
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libtiff
···
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nativeInstallCheckInputs = [ bc ];
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postPatch = ''
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patchShebangs ./build ./configure ./run_tests ./bin/*
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patchShebangs --build ./build ./configure ./run_tests
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patchShebangs --host ./bin/*
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# patching interpreters before fixup is needed for tests:
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patchShebangs ./bin/*
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patchShebangs testing/binaries/data/vectorstats/*py
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substituteInPlace ./run_tests \
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--replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""
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--replace-fail 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""
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# reduce build noise
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substituteInPlace ./configure \
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--replace-fail "[ '-Wall' ]" "[]"
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# fix error output (cuts off after a few lines otherwise)
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substituteInPlace ./build \
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--replace '"less -RX "' '"${less}/bin/less -RX "'
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--replace-fail 'stderr=subprocess.PIPE' 'stderr=None'
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'';
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configurePhase = ''
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export EIGEN_CFLAGS="-isystem ${eigen}/include/eigen3"
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runHook preConfigure
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export EIGEN_CFLAGS="-isystem ${eigen'}/include/eigen3"
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unset LD # similar to https://github.com/MRtrix3/mrtrix3/issues/1519
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./configure ${lib.optionalString (!withGui) "-nogui"};
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runHook postConfigure
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'';
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buildPhase = ''
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runHook preBuild
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./build
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(cd testing && ../build)
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runHook postBuild
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'';
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installCheckPhase = ''
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runHook preInstallCheck
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./run_tests units
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./run_tests binaries
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# can also `./run_tests scripts`, but this fails due to lack of FSL package
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# (and there's no convenient way to disable individual tests)
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runHook postInstallCheck
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'';
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doInstallCheck = true;
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···
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runHook postInstall
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'';
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postInstall = ''
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for prog in $out/bin/*; do
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if [[ -x "$prog" ]]; then
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wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
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fi
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done
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'';
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preFixup =
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if withGui then
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''
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qtWrapperArgs+=(--prefix PATH : ${lib.makeBinPath [ ants ]})
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''
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else
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''
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for prog in $out/bin/*; do
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if [[ -x "$prog" ]]; then
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wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
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fi
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done
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'';
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meta = with lib; {
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broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);