104 lines
2.8 KiB
Nix
104 lines
2.8 KiB
Nix
{ lib
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, stdenv
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, fetchurl
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, readline
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, xorg
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, mpi
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, cmake
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, bison
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, flex
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, git
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, perl
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, gsl
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, xcbuild
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, python3
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, useMpi ? false
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, useIv ? true
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, useCore ? false
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, useRx3d ? false
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}:
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stdenv.mkDerivation rec {
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pname = "neuron";
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version = "8.2.2";
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# format is for pythonModule conversion
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format = "other";
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nativeBuildInputs = [
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cmake
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bison
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flex
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git
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] ++ lib.optional useCore [ perl gsl ]
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++ lib.optional stdenv.isDarwin [ xcbuild ];
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buildInputs = lib.optional useIv [
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xorg.libX11.dev
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xorg.libXcomposite.dev
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xorg.libXext.dev
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];
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propagatedBuildInputs = [
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readline
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python3
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python3.pkgs.wheel
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python3.pkgs.setuptools
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python3.pkgs.scikit-build
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python3.pkgs.matplotlib
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] ++ lib.optional useMpi [
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mpi
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] ++ lib.optional useMpi [
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python3.pkgs.mpi4py
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] ++ lib.optional useRx3d [
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python3.pkgs.cython
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python3.pkgs.numpy
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];
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patches = [ ./neuron_darwin_rpath.patch ];
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# Patch build shells for cmake (bin, src, cmake) and submodules (external)
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postPatch = ''
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patchShebangs ./bin ./src ./external ./cmake
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sed -e 's#DESTDIR =#DESTDIR = '"$out"'#' -i external/coreneuron/extra/nrnivmodl_core_makefile.in
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'';
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cmakeFlags = [
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"-DNRN_ENABLE_INTERVIEWS=${if useIv then "ON" else "OFF"}"
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"-DNRN_ENABLE_MPI=${if useMpi then "ON" else "OFF"}"
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"-DNRN_ENABLE_CORENEURON=${if useCore then "ON" else "OFF"}"
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"-DNRN_ENABLE_RX3D=${if useRx3d then "ON" else "OFF"}"
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];
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postInstall = ''
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mkdir -p $out/${python3.sitePackages}
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mv $out/lib/python/* $out/${python3.sitePackages}/
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rm -rf $out/lib/python build
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for entry in $out/lib/*.so; do
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# remove references to build
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patchelf --set-rpath $(patchelf --print-rpath $entry | tr ':' '\n' | sed '/^\/build/d' | tr '\n' ':') $entry
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done
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'';
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src = fetchurl {
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url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz";
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sha256 = "sha256-orGeBxu3pu4AyAW5P1EGJv8G0dOUZcSOjpUaloqicZU=";
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};
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meta = with lib; {
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description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
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longDescription = ''
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NEURON is a simulation environment for developing and exercising models of
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neurons and networks of neurons. It is particularly well-suited to problems where
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cable properties of cells play an important role, possibly including extracellular
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potential close to the membrane), and where cell membrane properties are complex,
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involving many ion-specific channels, ion accumulation, and second messengers
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'';
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sourceProvenance = with sourceTypes; [ fromSource ];
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license = licenses.bsd3;
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homepage = "http://www.neuron.yale.edu/neuron";
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maintainers = with maintainers; [ adev davidcromp ];
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platforms = platforms.all;
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};
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}
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