1 files changed, 56 insertions, 22 deletions
diff --git a/shell.nix b/shell.nix
index 0d0a588..9c16281 100644
--- a/shell.nix
+++ b/shell.nix
@@ -1,26 +1,60 @@
 with import <nixpkgs> { };
-#https://github.com/NixOS/nixpkgs/archive/nixos-unstable.tar.gz
-#with import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/27212188ee8072ee79a4633e95fb5c731d40e1c0.tar.gz") { };
 let
-    R-packages = rWrapper.override { packages = with rPackages; [ ggplot2 Rtsne ]; };
-    gems = pkgs.bundlerEnv { name = "mutagenicity"; gemdir = ./.; };
-    lazar-gems = pkgs.bundlerEnv { name = "lazar"; gemdir = ./../lazar; };
-    latex-authblk = texlive.combine { inherit (texlive) scheme-medium preprint; };
-in pkgs.mkShell {
-    
-    buildInputs = with pkgs; [
-        fish
-        kakoune
-        cmake
-        git
-        latex-authblk
-        fontconfig
-        #haskellPackages.pandoc-placetable
-        haskellPackages.pandoc-crossref
-        haskellPackages.pandoc-citeproc
-        R-packages
-        lazar-gems
-        gems
-        gems.wrappedRuby
+  R-packages = rWrapper.override { packages = with rPackages; [ ggplot2 Rtsne ]; };
+  gems = bundlerEnv { name = "mustache"; gemdir = ./.; };
+  #lazar-gems = bundlerEnv { name = "lazar"; gemdir = ./../lazar; };
+  latex-authblk = texlive.combine { inherit (texlive) scheme-medium preprint; };
+  openbabel = stdenv.mkDerivation {
+
+    name = "openbabel-ruby";
+
+    src = fetchurl {
+      url = "https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/openbabel-3.1.1-source.tar.bz2";
+      sha256 = "puyDgdWeoypLJByLH715mstSvpSrZM29clBvtOInDmg=";
+    };
+
+    #outputs = [ "lib" ];
+
+    buildInputs = [
+      # openbabel
+      cmake
+      ruby
+      swig
+      boost
+      zlib
+      libxml2
+      cairo
+      eigen
+      pkg-config
+      pcre
     ];
+
+    configurePhase = ''
+      cmake . -DWITH_MAEPARSER=OFF -DWITH_JSON=OFF -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUN_SWIG=ON -DBINDINGS_ONLY=ON -DRUBY_BINDINGS=ON -DMINIMAL_BUILD=ON -DOPTIMIZE_NATIVE=ON -DCMAKE_INSTALL_PREFIX=$out  -DCMAKE_INSTALL_RPATH:STRING=$out/lib
+    '';
+
+    buildPhase = ''
+      make -j12
+    '';
+      
+  };
+in mkShell {
+  name = "mutagenicity-paper";
+  buildInputs = [
+    # paper
+    git
+    latex-authblk
+    fontconfig
+    #haskellPackages.pandoc-placetable
+    #haskellPackages.pandoc-csv2table
+    haskellPackages.pandoc-crossref
+    haskellPackages.pandoc-citeproc
+    #haskellPackages.pandoc-include
+    R-packages
+    #lazar-gems
+    gems
+    #gems.wrappedRuby
+    #openbabel-ruby
+    openbabel
+  ];
 }