1 files changed, 34 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
new file mode 100644
index 000000000000..4c32516b29f6
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
@@ -0,0 +1,34 @@
+{lib, stdenv, fetchurl, jre, unzip, makeWrapper}:
+
+stdenv.mkDerivation rec {
+  pname = "snpeff";
+  version = "4.3t";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/snpeff/snpEff_v${builtins.replaceStrings [ "." ] [ "_" ] version}_core.zip";
+    sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm";
+  };
+
+  nativeBuildInputs = [ makeWrapper unzip ];
+  buildInputs = [ jre ];
+
+  sourceRoot = "snpEff";
+
+  installPhase = ''
+    mkdir -p $out/libexec/snpeff
+    cp *.jar *.config $out/libexec/snpeff
+
+    mkdir -p $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/snpeff --add-flags "-jar $out/libexec/snpeff/snpEff.jar"
+    makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar"
+  '';
+
+  meta = with lib; {
+    description = "Genetic variant annotation and effect prediction toolbox";
+    license = licenses.lgpl3;
+    homepage = "http://snpeff.sourceforge.net/";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.all;
+  };
+
+}