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{ lib
, stdenv
, fetchurl
, readline
, xorg
, mpi
, cmake
, bison
, flex
, git
, perl
, gsl
, xcbuild
, python3
, useMpi ? false
, useIv ? true
, useCore ? false
, useRx3d ? false
}:
stdenv.mkDerivation rec {
pname = "neuron";
version = "8.2.3";
# format is for pythonModule conversion
format = "other";
nativeBuildInputs = [
cmake
bison
flex
git
] ++ lib.optionals useCore [ perl gsl ]
++ lib.optionals stdenv.isDarwin [ xcbuild ];
buildInputs = lib.optionals useIv [
xorg.libX11.dev
xorg.libXcomposite.dev
xorg.libXext.dev
];
propagatedBuildInputs = [
readline
python3
python3.pkgs.wheel
python3.pkgs.setuptools
python3.pkgs.scikit-build
python3.pkgs.matplotlib
] ++ lib.optionals useMpi [
mpi
] ++ lib.optionals useMpi [
python3.pkgs.mpi4py
] ++ lib.optionals useRx3d [
python3.pkgs.cython
python3.pkgs.numpy
];
patches = [ ./neuron_darwin_rpath.patch ];
# Patch build shells for cmake (bin, src, cmake) and submodules (external)
postPatch = ''
patchShebangs ./bin ./src ./external ./cmake
sed -e 's#DESTDIR =#DESTDIR = '"$out"'#' -i external/coreneuron/extra/nrnivmodl_core_makefile.in
'';
cmakeFlags = [
"-DNRN_ENABLE_INTERVIEWS=${if useIv then "ON" else "OFF"}"
"-DNRN_ENABLE_MPI=${if useMpi then "ON" else "OFF"}"
"-DNRN_ENABLE_CORENEURON=${if useCore then "ON" else "OFF"}"
"-DNRN_ENABLE_RX3D=${if useRx3d then "ON" else "OFF"}"
];
postInstall = ''
mkdir -p $out/${python3.sitePackages}
mv $out/lib/python/* $out/${python3.sitePackages}/
rm -rf $out/lib/python build
for entry in $out/lib/*.so; do
# remove references to build
patchelf --set-rpath $(patchelf --print-rpath $entry | tr ':' '\n' | sed '/^\/build/d' | tr '\n' ':') $entry
done
'';
src = fetchurl {
url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz";
sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI=";
};
meta = with lib; {
description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
longDescription = ''
NEURON is a simulation environment for developing and exercising models of
neurons and networks of neurons. It is particularly well-suited to problems where
cable properties of cells play an important role, possibly including extracellular
potential close to the membrane), and where cell membrane properties are complex,
involving many ion-specific channels, ion accumulation, and second messengers
'';
sourceProvenance = with sourceTypes; [ fromSource ];
license = licenses.bsd3;
homepage = "http://www.neuron.yale.edu/neuron";
maintainers = with maintainers; [ adev davidcromp ];
platforms = platforms.all;
};
}
|