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Diffstat (limited to 'nixpkgs/pkgs/applications/science/physics/crystfel/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/physics/crystfel/default.nix | 242 |
1 files changed, 242 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix b/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix new file mode 100644 index 000000000000..92b48ec86309 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix @@ -0,0 +1,242 @@ +{ 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; + }; + +} |