namd: Convert to new overlay system

pkgs/all-packages.nix

@@ -12,4 +12,6 @@ self: pkgs: with pkgs; {
   openslide-python = callPackage ./openslide/python.nix { };
 
   sumo = callPackage ./sumo.nix { };
+
+  namd = callPackage ./namd.nix { };
 }

pkgs/namd.nix

@@ -0,0 +1,55 @@
+{ stdenv, fetchurl
+, bash, tcsh }:
+
+stdenv.mkDerivation rec {
+  version = "2.11";
+  name = "namd-${version}";
+
+  src = fetchurl {
+    url = "http://ppomorsk.sharcnet.ca/namd-${version}.tar.gz";
+    sha256 = "1ylrxy8iqmsr64z82nr9cf3vvq9hbdav128fs2czm46y999dpls1";
+  };
+
+  postUnpack = ''
+    cd namd-${version}
+    tar -xf charm-*.tar
+    tar -xzf fftw-linux-x86_64.tar.gz
+    mv linux-x86_64 fftw
+    tar -xzf tcl*-linux-x86_64.tar.gz
+    mv tcl*-linux-x86_64 tcl
+    tar -xzf tcl*-linux-x86_64-threaded.tar.gz
+    mv tcl*-linux-x86_64-threaded tcl-threaded
+    cd ..
+  '';
+  patchPhase = ''
+    find charm-*/ -type f | xargs sed -i \
+      -e 's,/bin/cp,cp,g' \
+      -e 's,/bin/rm,rm,g' \
+      -e 's,/lib/cpp,cpp,g'
+  '';
+  configurePhase = ''
+    tcsh -f ./config  Linux-x86_64-g++   --charm-arch multicore-linux64
+  '';
+  buildPhase = ''
+    cd charm-*/
+    ./build charm++ multicore-linux64 --no-build-shared --with-production
+    cd ..
+    cd Linux-x86_64-g++
+    make
+    cd ..
+  '';
+  installPhase = ''
+    rm -fr Linux-x86_64-g++/{obj,src,inc,Make*,plugins,sb}
+    cp -r plugins Linux-x86_64-g++/
+    cp -r psfgen Linux-x86_64-g++/sb
+    mkdir -p $out/lib/namd
+    cp -r Linux-x86_64-g++/* $out/lib/namd
+    mkdir -p $out/bin
+    ln -s $out/lib/namd/namd2 $out/bin/namd2
+  '';
+
+  buildInputs = [
+    bash
+    tcsh
+  ];
+}