diff options
Diffstat (limited to 'pkgs/applications/science/biology/mrtrix/default.nix')
-rw-r--r-- | pkgs/applications/science/biology/mrtrix/default.nix | 31 |
1 files changed, 23 insertions, 8 deletions
diff --git a/pkgs/applications/science/biology/mrtrix/default.nix b/pkgs/applications/science/biology/mrtrix/default.nix index 6959b2caab8a..528277e05e38 100644 --- a/pkgs/applications/science/biology/mrtrix/default.nix +++ b/pkgs/applications/science/biology/mrtrix/default.nix @@ -1,17 +1,17 @@ { stdenv, lib, fetchFromGitHub, python, makeWrapper -, eigen, fftw, libtiff, zlib, ants, bc +, eigen, fftw, libtiff, libpng, zlib, ants, bc , qt5, libGL, libGLU, libX11, libXext , withGui ? true }: stdenv.mkDerivation rec { pname = "mrtrix"; - version = "3.0_RC3_latest"; + version = "3.0.0"; src = fetchFromGitHub { owner = "MRtrix3"; repo = "mrtrix3"; rev = version; - sha256 = "184nv524p8j94qicjy9l288bqcgl2yxqqs55a7042i0gfsnwp51c"; + sha256 = "1vvmmbw3m0bdfwp4szr62ygzsvkj0ss91cx5zlkspsr1rff05f9b"; fetchSubmodules = true; }; @@ -22,7 +22,9 @@ stdenv.mkDerivation rec { python fftw libtiff - zlib ] ++ lib.optionals withGui [ + libpng + zlib + ] ++ lib.optionals withGui [ libGL libGLU libX11 @@ -34,9 +36,14 @@ stdenv.mkDerivation rec { installCheckInputs = [ bc ]; postPatch = '' - patchShebangs ./build ./configure ./run_tests ./bin/population_template + 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 >> $LOGFILE 2>&1' "" + --replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' "" ''; configurePhase = '' @@ -50,7 +57,13 @@ stdenv.mkDerivation rec { (cd testing && ../build) ''; - installCheckPhase = "./run_tests"; + 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 = '' @@ -63,7 +76,9 @@ stdenv.mkDerivation rec { postInstall = '' for prog in $out/bin/*; do - wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]} + if [[ -x "$prog" ]]; then + wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]} + fi done ''; |