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{ lib
, stdenv
, fetchurl
, fetchFromGitHub
, fetchpatch
, fetchzip
, cmake
, lz4
, bzip2
, m4
, hdf5
, gsl
, unzip
, makeWrapper
, meson
, git
, ninja
, eigen
, pkg-config
, wrapGAppsHook
, flex
, bison
, doxygen
, opencl-headers
, ncurses
, msgpack
, fftw
, zeromq
, ocl-icd
, gtk3
, gdk-pixbuf
, argp-standalone
, memorymappingHook
, withGui ? true
, withBitshuffle ? true
}:
let
libccp4 = stdenv.mkDerivation rec {
pname = "libccp4";
version = "8.0.0";
src = fetchurl {
url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
};
nativeBuildInputs = [ meson ninja ];
buildInputs = [ hdf5 gsl ];
configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
# preprocessor flag.
env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";
patches = [
./libccp4-use-hardcoded-syminfo-lib.patch
];
postPatch =
let
mesonPatch = fetchzip {
url = "https://wrapdb.mesonbuild.com/v2/libccp4c_8.0.0-1/get_patch#somefile.zip";
hash = "sha256-ohskfKh+972Pl56KtwAeWwHtAaAFNpCzz5vZBAI/vdU=";
};
in
''
cp ${mesonPatch}/meson.build .
'';
};
# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
# since the build process is very hard-coded for a specific machine, architecture, and libraries.
mosflm =
let
version = "7.4.0";
src =
if stdenv.isDarwin then
fetchurl
{
url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-osx-64-noX11.zip";
sha256 = "1da5wimv3kl8bccp49j69vh8gi28cn7axg59lrmb38s68c618h7j";
}
else
fetchurl {
url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-linux-64-noX11.zip";
hash = "sha256:1f2qins5kaz5v6mkaclncqpirx3mlz177ywm13py9p6s9mk99g32";
};
mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";
in
stdenv.mkDerivation rec {
pname = "mosflm";
inherit version src;
dontBuild = true;
nativeBuildInputs = [ unzip makeWrapper ];
sourceRoot = ".";
# mosflm statically links against its own libccp4, which as the syminfo.lib environment variable problem.
# Here, we circumvent it by creating a little wrapper script that calls mosflm after setting the SYMINFO variable.
installPhase = ''
mkdir -p $out/bin
cp ${mosflmBinary} $out/bin/mosflm-raw
makeWrapper $out/bin/mosflm-raw $out/bin/mosflm --set SYMINFO ${libccp4}/share/syminfo.lib --add-flags -n
'';
};
xgandalf = stdenv.mkDerivation rec {
pname = "xgandalf";
version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b";
src = fetchurl {
url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E=";
};
nativeBuildInputs = [ meson pkg-config ninja ];
buildInputs = [ eigen ];
};
pinkIndexer = stdenv.mkDerivation rec {
pname = "pinkindexer";
version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503";
src = fetchurl {
url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0=";
};
nativeBuildInputs = [ meson pkg-config ninja ];
buildInputs = [ eigen ];
};
fdip = stdenv.mkDerivation rec {
pname = "fdip";
version = "5628fedddd79323b4b26df9b85e9543d83286d4c";
src = fetchurl {
url = "https://gitlab.desy.de/thomas.white/fdip/-/archive/${version}/fdip-${version}.tar.gz";
hash = "sha256-EaihnW7p//ecgMn+KKlfmBeXrnAqs+HdhN+ovuSrtiQ=";
};
nativeBuildInputs = [ meson ninja pkg-config ];
buildInputs = [ eigen ];
};
hdf5-external-filter-plugins = stdenv.mkDerivation rec {
pname = "HDF5-External-Filter-Plugins";
version = "0.1.0";
src = fetchFromGitHub {
owner = "nexusformat";
repo = pname;
rev = "49e3b65eca772bca77af13ba047d8b577673afba";
hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI=";
};
patches = [
(fetchpatch {
url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch";
hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo=";
})
];
nativeBuildInputs = [ cmake ];
buildInputs = [ hdf5 lz4 bzip2 ];
cmakeFlags = [
"-DENABLE_BITSHUFFLE_PLUGIN=yes"
"-DENABLE_LZ4_PLUGIN=yes"
"-DENABLE_BZIP2_PLUGIN=yes"
];
};
in
stdenv.mkDerivation rec {
pname = "crystfel";
version = "0.10.2";
src = fetchurl {
url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4=";
};
nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]
++ lib.optionals withGui [ wrapGAppsHook ];
buildInputs = [
hdf5
gsl
ncurses
msgpack
fftw
fdip
zeromq
ocl-icd
libccp4
mosflm
pinkIndexer
xgandalf
] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
++ lib.optionals stdenv.isDarwin [
argp-standalone
] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [
memorymappingHook
]
++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];
patches = [
./link-to-argp-standalone-if-needed.patch
./disable-fmemopen-on-aarch64-darwin.patch
(fetchpatch {
url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
})
];
# CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
# we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just
# hard-code mosflm's path once.
postPatch = ''
sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
'';
postInstall = lib.optionalString withBitshuffle ''
for file in $out/bin/*; do
wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
done
'';
meta = with lib; {
description = "Data processing for serial crystallography";
longDescription = ''
CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data from "serial crystallography" experiments, often (but not always) performed using an X-ray Free-Electron Laser. Compared to rotation data, some of the particular characteristics of such data which call for a specialised software suite are:
- The sliced, rather than integrated, measurement of intensity data. Many, if not all reflections are partially integrated.
- Many patterns (thousands) are required - high throughput is needed.
- The crystal orientations in each pattern are random and uncorrelated.
- Merging into lower symmetry point groups may require the resolution of indexing ambiguities.'';
homepage = "https://www.desy.de/~twhite/crystfel/";
changelog = "https://www.desy.de/~twhite/crystfel/changes.html";
downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
license = licenses.gpl3Plus;
maintainers = with maintainers; [ pmiddend ];
platforms = platforms.unix;
};
}
|