diff options
Diffstat (limited to 'pkgs/applications/science/physics/crystfel/default.nix')
| -rw-r--r-- | pkgs/applications/science/physics/crystfel/default.nix | 54 |
1 files changed, 36 insertions, 18 deletions
diff --git a/pkgs/applications/science/physics/crystfel/default.nix b/pkgs/applications/science/physics/crystfel/default.nix index 92b48ec863091..e7eb69fb4e1c1 100644 --- a/pkgs/applications/science/physics/crystfel/default.nix +++ b/pkgs/applications/science/physics/crystfel/default.nix @@ -6,18 +6,19 @@ , fetchzip , cmake , lz4 +, gfortran , bzip2 -, m4 , hdf5 , gsl , unzip , makeWrapper +, zlib , meson -, git , ninja +, pandoc , eigen , pkg-config -, wrapGAppsHook +, wrapGAppsHook3 , flex , bison , doxygen @@ -40,7 +41,7 @@ let pname = "libccp4"; version = "8.0.0"; src = fetchurl { - url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz"; + url = "https://ftp.ccp4.ac.uk/opensource/libccp4-${version}.tar.gz"; hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0="; }; nativeBuildInputs = [ meson ninja ]; @@ -87,7 +88,7 @@ let }; mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11"; in - stdenv.mkDerivation rec { + stdenv.mkDerivation { pname = "mosflm"; inherit version src; @@ -111,7 +112,7 @@ let pname = "xgandalf"; version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b"; src = fetchurl { - url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; + url = "https://gitlab.desy.de/thomas.white/xgandalf/-/archive/${version}/xgandalf-${version}.tar.gz"; hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E="; }; @@ -121,10 +122,10 @@ let pinkIndexer = stdenv.mkDerivation rec { pname = "pinkindexer"; - version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503"; + version = "15caa21191e27e989b750b29566e4379bc5cd21a"; src = fetchurl { url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; - hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0="; + hash = "sha256-v/SCJiHAV05Lc905y/dE8uBXlW+lLX9wau4XORYdbQg="; }; nativeBuildInputs = [ meson pkg-config ninja ]; @@ -169,16 +170,30 @@ let "-DENABLE_BZIP2_PLUGIN=yes" ]; }; + + millepede-ii = stdenv.mkDerivation rec { + pname = "millepede-ii"; + version = "04-13-06"; + src = fetchurl { + url = "https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V${version}/millepede-ii-V${version}.tar.gz"; + hash = "sha256-aFoo8AGBsUEN2u3AmnSpTqJ6JeNV6j9vkAFTZ34I+sI="; + }; + + nativeBuildInputs = [ gfortran ]; + buildInputs = [ zlib ]; + + makeFlags = [ "PREFIX=$(out)" ]; + }; in stdenv.mkDerivation rec { pname = "crystfel"; - version = "0.10.2"; + version = "0.11.0"; src = fetchurl { - url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz"; - sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4="; + url = "https://www.desy.de/~twhite/crystfel/crystfel-${version}.tar.gz"; + sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc="; }; nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ] - ++ lib.optionals withGui [ wrapGAppsHook ]; + ++ lib.optionals withGui [ wrapGAppsHook3 ]; buildInputs = [ hdf5 gsl @@ -192,6 +207,7 @@ stdenv.mkDerivation rec { mosflm pinkIndexer xgandalf + pandoc ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ] ++ lib.optionals stdenv.isDarwin [ argp-standalone @@ -201,12 +217,12 @@ stdenv.mkDerivation rec { ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ]; patches = [ + # on darwin at least, we need to link to a separate argp library; + # this patch adds a test for this and the necessary linker options ./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="; - }) + # hotfix for an issue that occurs (at least) on NixOS: + # if the temporary path is too long, we get a segfault + ./gui-path-issue.patch ]; # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but @@ -218,7 +234,9 @@ stdenv.mkDerivation rec { postInstall = lib.optionalString withBitshuffle '' for file in $out/bin/*; do - wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins + wrapProgram $file \ + --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins \ + --prefix PATH ":" ${lib.makeBinPath [ millepede-ii ]} done ''; |