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with import <nixpkgs> { };
let
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
];
}
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