nixpkgs/pkgs/applications/science/biology/neuron/default.nix
Robert Scott e0aec554eb pythonPackages.neuron: fix for darwin
un-compensate for some of the darwin quirks the neuron
source is expecting
2019-06-09 12:18:58 +02:00

87 lines
3.1 KiB
Nix

{ stdenv
, fetchurl
, pkgconfig
, automake
, autoconf
, libtool
, ncurses
, readline
, which
, python ? null
, mpi ? null
, iv
}:
stdenv.mkDerivation rec {
name = "neuron-${version}";
version = "7.5";
nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
buildInputs = [ ncurses readline python mpi iv ];
src = fetchurl {
url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
sha256 = "0f26v3qvzblcdjg7isq0m9j2q8q7x3vhmkfllv8lsr3gyj44lljf";
};
patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
# With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
postPatch = stdenv.lib.optionalString stdenv.cc.isClang ''
substituteInPlace src/gnu/neuron_gnu_builtin.h \
--replace 'double abs(double arg);' "" \
--replace 'float abs(float arg);' "" \
--replace 'short abs(short arg);' "" \
--replace 'long abs(long arg);' ""
'' + stdenv.lib.optionalString stdenv.isDarwin ''
# we are darwin, but we don't have all the quirks the source wants to compensate for
substituteInPlace src/nrnpython/setup.py.in --replace 'readline="edit"' 'readline="readline"'
for f in src/nrnpython/*.[ch] ; do
substituteInPlace $f --replace "<Python/Python.h>" "<Python.h>"
done
'';
enableParallelBuilding = true;
## neuron install by default everything under prefix/${host_arch}/*
## override this to support nix standard file hierarchy
## without issues: install everything under prefix/
preConfigure = ''
./build.sh
export prefix="''${prefix} --exec-prefix=''${out}"
'';
configureFlags = with stdenv.lib;
[ "--with-readline=${readline}" "--with-iv=${iv}" ]
++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
else ["--without-mpi"]);
postInstall = stdenv.lib.optionals (python != null) [ ''
## standardise python neuron install dir if any
if [[ -d $out/lib/python ]]; then
mkdir -p ''${out}/${python.sitePackages}
mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/
fi
''];
propagatedBuildInputs = [ readline ncurses which libtool ];
meta = with stdenv.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";
license = licenses.bsd3;
homepage = http://www.neuron.yale.edu/neuron;
maintainers = [ maintainers.adev ];
platforms = platforms.all;
};
}