CrystFEL: init at 0.10.1
This commit is contained in:
Philipp Middendorf
parent
fb679d351a
commit
93332c2779
5 changed files with 329 additions and 0 deletions
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@ -0,0 +1,43 @@
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Description: Fixing argument mismatches in Fortran code, addressing #957430.
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Author: Andrius Merkys <merkys@debian.org>
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Forwarded: ccp4-dev@dl.ac.uk
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--- a/fortran/pack_f.f
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+++ b/fortran/pack_f.f
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@@ -106,7 +106,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call pack_wordimage_f(data, x, y, filnarray)
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+ call pack_longimage_f(data, x, y, filnarray)
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return
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end
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@@ -138,7 +138,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call v2pack_wordimage_f(data, x, y, filnarray)
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+ call v2pack_longimage_f(data, x, y, filnarray)
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return
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end
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--- a/fortran/lgglib.f
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+++ b/fortran/lgglib.f
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@@ -1236,7 +1236,7 @@
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B3(2) = XYZ(2) * CELL(2)
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B3(3) = XYZ(3) * CELL(3)
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C
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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c
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c
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@@ -1274,7 +1274,7 @@
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B3(1) = XYZ(1)
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B3(2) = XYZ(2)
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B3(3) = XYZ(3)
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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character*80 function getnam(filnam)
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character*(*) filnam
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226
pkgs/applications/science/physics/crystfel/default.nix
Normal file
226
pkgs/applications/science/physics/crystfel/default.nix
Normal file
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@ -0,0 +1,226 @@
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{ lib
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, stdenv
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, fetchurl
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, fetchFromGitHub
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, cmake
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, lz4
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, bzip2
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, gfortran
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, m4
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, hdf5
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, gsl
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, slurm
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, unzip
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, makeWrapper
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, meson
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, git
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, ninja
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, eigen
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, pkg-config
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, wrapGAppsHook
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, flex
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, bison
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, doxygen
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, opencl-headers
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, ncurses
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, msgpack
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, fftw
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, zeromq
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, ocl-icd
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, gtk3
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, gdk-pixbuf
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, argp-standalone
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, memorymappingHook
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, withGui ? true
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, withBitshuffle ? true
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}:
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let
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libccp4 = stdenv.mkDerivation rec {
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pname = "libccp4";
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version = "6.5.1";
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src = fetchurl {
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# Original mirror, now times out
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# url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
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sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
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};
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nativeBuildInputs = [ gfortran m4 ];
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buildInputs = [ hdf5 gsl ];
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configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
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# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
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# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
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# preprocessor flag.
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preBuild = ''
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makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"$out/share/syminfo.lib\"')
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export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
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'';
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makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
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patches = [
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./libccp4-use-hardcoded-syminfo-lib.patch
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./0002-fix-ftbfs-with-gcc-10.patch
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];
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};
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# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
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# since the build process is very hard-coded for a specific machine, architecture, and libraries.
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mosflm =
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let
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version = "7.4.0";
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src =
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if stdenv.isDarwin then
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fetchurl
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{
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url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-osx-64-noX11.zip";
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sha256 = "1da5wimv3kl8bccp49j69vh8gi28cn7axg59lrmb38s68c618h7j";
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}
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else
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fetchurl {
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url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-linux-64-noX11.zip";
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sha256 = "1rqh3nprxfmnyihllw31nb8i3wfhybmsic6y7z6wn4rafyv3w4fk";
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};
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mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";
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in
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stdenv.mkDerivation rec {
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pname = "mosflm";
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inherit version src;
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dontBuild = true;
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nativeBuildInputs = [ unzip makeWrapper ];
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sourceRoot = ".";
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# mosflm statically links against its own libccp4, which as the syminfo.lib environment variable problem.
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# Here, we circumvent it by creating a little wrapper script that calls mosflm after setting the SYMINFO variable.
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installPhase = ''
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mkdir -p $out/bin
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cp ${mosflmBinary} $out/bin/mosflm-raw
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makeWrapper $out/bin/mosflm-raw $out/bin/mosflm --set SYMINFO ${libccp4}/share/syminfo.lib --add-flags -n
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'';
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};
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xgandalf = stdenv.mkDerivation rec {
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pname = "xgandalf";
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version = "c15afa2381d5f87d4aefcc8181a15b4a6fd3a955";
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src = fetchurl {
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
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sha256 = "11i1w57a3rpnb4x5y4n8d3iffn5m9w1zydl69syzljdk3aqg2pv8";
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};
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nativeBuildInputs = [ meson pkg-config ninja ];
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buildInputs = [ eigen ];
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};
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pinkIndexer = stdenv.mkDerivation rec {
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pname = "pinkindexer";
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version = "8a828788f8272a89d484b00afbd2500c2c1ff974";
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src = fetchurl {
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
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sha256 = "1mkgf1xd91ay0z0632kzxm0z3wcxf0cayjvs6a3znds72dkhfsyh";
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};
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nativeBuildInputs = [ meson pkg-config ninja ];
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buildInputs = [ eigen ];
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};
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fdip = stdenv.mkDerivation rec {
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pname = "fdip";
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version = "29da626f17f66d5c0780fc59b1eafb7c85b81dd6";
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src = fetchurl {
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url = "https://gitlab.desy.de/philipp.middendorf/fdip/-/archive/${version}/fdip-${version}.tar.gz";
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sha256 = "184l76r4fgznq54rnhgjk7dg41kqdl0d1da02vr5y4cs2fyqppky";
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};
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nativeBuildInputs = [ meson ninja pkg-config ];
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buildInputs = [ eigen ];
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};
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hdf5-external-filter-plugins = stdenv.mkDerivation rec {
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pname = "HDF5-External-Filter-Plugins";
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version = "0.1.0";
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src = fetchFromGitHub {
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owner = "nexusformat";
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repo = pname;
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rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
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sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
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};
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nativeBuildInputs = [ cmake ];
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buildInputs = [ hdf5 lz4 bzip2 ];
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cmakeFlags = [
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"-DENABLE_BITSHUFFLE_PLUGIN=yes"
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"-DENABLE_LZ4_PLUGIN=yes"
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"-DENABLE_BZIP2_PLUGIN=yes"
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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 = "crystfel";
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version = "0.10.1";
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src = fetchurl {
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url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
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sha256 = "0i9d5ggalic7alj97dxjdys7010kxhm2cb4lwakvigl023j8ms79";
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};
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nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers ]
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++ lib.optionals withGui [ wrapGAppsHook ];
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buildInputs = [
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hdf5
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gsl
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ncurses
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msgpack
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fftw
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fdip
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zeromq
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ocl-icd
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libccp4
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mosflm
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pinkIndexer
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xgandalf
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] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
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++ lib.optionals stdenv.isDarwin [
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argp-standalone
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memorymappingHook
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]
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# slurm is not available for Darwin; when it is, remove the condition
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++ lib.optionals (!stdenv.isDarwin) [ slurm ]
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# hdf5-external-filter-plugins doesn't link on Darwin
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++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
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patches = [ ./link-to-argp-standalone-if-needed.patch ];
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# CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
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# we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just
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# hard-code mosflm's path once.
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postPatch = ''
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sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
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|
'';
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postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
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for file in $out/bin/*; do
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wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
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|
done
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|
'';
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meta = with lib; {
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description = "Data processing for serial crystallography";
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longDescription = ''
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|
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:
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- The sliced, rather than integrated, measurement of intensity data. Many, if not all reflections are partially integrated.
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- Many patterns (thousands) are required - high throughput is needed.
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- The crystal orientations in each pattern are random and uncorrelated.
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- Merging into lower symmetry point groups may require the resolution of indexing ambiguities.'';
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homepage = "https://www.desy.de/~twhite/crystfel/";
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changelog = "https://www.desy.de/~twhite/crystfel/changes.html";
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|
downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
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|
license = licenses.gpl3Plus;
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|
maintainers = with maintainers; [ pmiddend ];
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|
platforms = [ "x86_64-linux" "x86_64-darwin" ];
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|
};
|
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|
|
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|
}
|
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|
@ -0,0 +1,30 @@
|
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|
diff --git a/ccp4/csymlib.c b/ccp4/csymlib.c
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|
index 76bc70b..7a0c5dc 100644
|
||||||
|
--- a/ccp4/csymlib.c
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||||||
|
+++ b/ccp4/csymlib.c
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|
@@ -137,24 +137,7 @@ CCP4SPG *ccp4spg_load_spacegroup(const int numspg, const int ccp4numspg,
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|
}
|
||||||
|
|
||||||
|
/* Open the symop file: */
|
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|
- if (!(symopfile = getenv("SYMINFO"))) {
|
||||||
|
- if (debug)
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|
- printf("Environment variable SYMINFO not set ... guessing location of symmetry file. \n");
|
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|
- if (!(ccp4dir = getenv("CLIBD"))) {
|
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|
- printf("Environment variable CLIBD not set ... big trouble! \n");
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|
- return NULL;
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|
- }
|
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|
-
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|
- symopfile = ccp4_utils_malloc((strlen(ccp4dir)+22)*sizeof(char));
|
||||||
|
- strcpy(symopfile,ccp4_utils_joinfilenames(ccp4dir,"syminfo.lib"));
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||||||
|
- symopfile[strlen(ccp4dir)+21] = '\0';
|
||||||
|
- ccp4printf(1," SYMINFO file set to %s \n",symopfile);
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|
- } else {
|
||||||
|
- if (debug) {
|
||||||
|
- ccp4printf(1,"\n Spacegroup information obtained from library file: \n");
|
||||||
|
- ccp4printf(1," Logical Name: SYMINFO Filename: %s\n\n",symopfile);
|
||||||
|
- }
|
||||||
|
- }
|
||||||
|
+ symopfile = NIX_PROVIDED_SYMOP_FILE;
|
||||||
|
|
||||||
|
filein = fopen(symopfile,"r");
|
||||||
|
if (!filein) {
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
diff --git a/meson.build b/meson.build
|
||||||
|
index efc9002b..070f37e4 100644
|
||||||
|
--- a/meson.build
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||||||
|
+++ b/meson.build
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||||||
|
@@ -34,6 +34,12 @@ if slurmdep.found()
|
||||||
|
conf_data.set10('HAVE_SLURM', 1)
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|
endif
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||||||
|
|
||||||
|
+if build_machine.system() == 'darwin' or build_machine.system() == 'freebsd' or not cc.links('#include <argp.h>\nstatic error_t parse_opt (int key, char *arg, struct argp_state *state) { argp_usage(state); return 0; }; void main() {}')
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|
+ argpdep = cc.find_library('argp')
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||||||
|
+else
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||||||
|
+ argpdep = dependency('', required : false)
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||||||
|
+endif
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|
+
|
||||||
|
# Find HDF5 using inbuilt Meson methods. Requires Meson >= 0.50.0
|
||||||
|
hdf5dep = dependency('hdf5', language: 'c', required: true)
|
||||||
|
|
||||||
|
@@ -180,7 +186,7 @@ if zmqdep.found()
|
||||||
|
endif
|
||||||
|
|
||||||
|
executable('indexamajig', indexamajig_sources,
|
||||||
|
- dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep],
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|
+ dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep, argpdep],
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||||||
|
install: true,
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||||||
|
install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')
|
||||||
|
|
||||||
|
|
@ -1910,6 +1910,10 @@ with pkgs;
|
||||||
|
|
||||||
checkip = callPackage ../tools/networking/checkip { };
|
checkip = callPackage ../tools/networking/checkip { };
|
||||||
|
|
||||||
|
crystfel = callPackage ../applications/science/physics/crystfel { };
|
||||||
|
|
||||||
|
crystfel-headless = callPackage ../applications/science/physics/crystfel { withGui = false; };
|
||||||
|
|
||||||
ec2-api-tools = callPackage ../tools/virtualization/ec2-api-tools { };
|
ec2-api-tools = callPackage ../tools/virtualization/ec2-api-tools { };
|
||||||
|
|
||||||
ec2-ami-tools = callPackage ../tools/virtualization/ec2-ami-tools { };
|
ec2-ami-tools = callPackage ../tools/virtualization/ec2-ami-tools { };
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue