neuron: enable GUI

NixOS · Jun 28, 2017 · 24c59a4 · 24c59a4
1 parent 46a4462
commit 24c59a4
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Showing 3 changed files with 40 additions and 2 deletions.
diff --git a/pkgs/applications/science/biology/iv/default.nix b/pkgs/applications/science/biology/iv/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchurl, neuron-version
+, libX11, libXext, patchelf
+}:
+
+stdenv.mkDerivation rec
+  { name = "iv-19";
+    src = fetchurl
+      { url = "http://www.neuron.yale.edu/ftp/neuron/versions/v${neuron-version}/${name}.tar.gz";
+        sha256 = "1q22vjngvn3m61mjxynkik7pxvsgc9a0ym46qpa84hmz1v86mdrw";
+      };
+    nativeBuildInputs = [ patchelf ];
+    buildInputs = [ libXext ];
+    propagatedBuildInputs = [ libX11 ];
+    hardeningDisable = [ "format" ];
+    postInstall = ''
+      for dir in $out/*; do # */
+        if [ -d $dir/lib ]; then
+	  mv $dir/* $out # */
+          rmdir $dir
+          break
+        fi
+      done
+      patchelf --add-needed ${libX11}/lib/libX11.so $out/lib/libIVhines.so
+    '';
+    meta = with stdenv.lib;
+      { description = "InterViews graphical library for Neuron";
+        license     = licenses.bsd3;
+        homepage    = http://www.neuron.yale.edu/neuron;
+        platforms   = platforms.all;
+      };
+  }
diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix
@@ -9,14 +9,15 @@
 , which
 , python ? null
 , mpi ? null
+, iv
 }:
 
 stdenv.mkDerivation rec {
   name = "neuron-${version}";
   version = "7.4";
 
   nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
-  buildInputs = [ ncurses readline python mpi  ];
+  buildInputs = [ ncurses readline python mpi iv ];
 
   src = fetchurl {
     url = "http://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
@@ -45,7 +46,7 @@ stdenv.mkDerivation rec {
   '';
 
   configureFlags = with stdenv.lib;
-                    [ "--without-x" "--with-readline=${readline}" ]
+                    [ "--with-readline=${readline}" "--with-iv=${iv}" ]
                     ++  optionals (python != null)  [ "--with-nrnpython=${python.interpreter}" ]
                     ++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
                         else ["--without-mpi"]);

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
@@ -17659,6 +17659,10 @@ with pkgs;
 
   igv = callPackage ../applications/science/biology/igv { };
 
+  iv = callPackage ../applications/science/biology/iv {
+    neuron-version = neuron.version;
+  };
+
   neuron = callPackage ../applications/science/biology/neuron {
     python = null;
   };
@@ -17667,6 +17671,8 @@ with pkgs;
     mpi = pkgs.openmpi;
   });
 
+  neuron-full = neuron-mpi.override { inherit python; };
+
   mrbayes = callPackage ../applications/science/biology/mrbayes { };
 
   minc_tools = callPackage ../applications/science/biology/minc-tools { };