diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/neuron/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/biology/neuron/default.nix | 27 |
1 files changed, 14 insertions, 13 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix index 8cad5f466c5f..7bfef3a82fed 100644 --- a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix @@ -1,6 +1,6 @@ -{ stdenv +{ lib, stdenv , fetchurl -, pkgconfig +, pkg-config , automake , autoconf , libtool @@ -8,7 +8,8 @@ , readline , which , python ? null -, mpi ? null +, useMpi ? false +, mpi , iv }: @@ -16,24 +17,25 @@ stdenv.mkDerivation rec { pname = "neuron"; version = "7.5"; - nativeBuildInputs = [ which pkgconfig automake autoconf libtool ]; - buildInputs = [ ncurses readline python mpi iv ]; + nativeBuildInputs = [ which pkg-config automake autoconf libtool ]; + buildInputs = [ ncurses readline python iv ] + ++ lib.optional useMpi mpi; 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 ]); + patches = (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 '' + postPatch = 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 '' + '' + 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 @@ -51,14 +53,14 @@ stdenv.mkDerivation rec { export prefix="''${prefix} --exec-prefix=''${out}" ''; - configureFlags = with stdenv.lib; + configureFlags = with lib; [ "--with-readline=${readline}" "--with-iv=${iv}" ] ++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ] - ++ (if mpi != null then ["--with-mpi" "--with-paranrn"] + ++ (if useMpi then ["--with-mpi" "--with-paranrn"] else ["--without-mpi"]); - postInstall = stdenv.lib.optionals (python != null) [ '' + postInstall = lib.optionals (python != null) [ '' ## standardise python neuron install dir if any if [[ -d $out/lib/python ]]; then mkdir -p ''${out}/${python.sitePackages} @@ -68,7 +70,7 @@ stdenv.mkDerivation rec { propagatedBuildInputs = [ readline ncurses which libtool ]; - meta = with stdenv.lib; { + 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 @@ -84,4 +86,3 @@ stdenv.mkDerivation rec { platforms = platforms.x86_64 ++ platforms.i686; }; } - |