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{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";
};
buildInputs = [ unzip jre makeWrapper ];
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 stdenv.lib; {
description = "Genetic variant annotation and effect prediction toolbox.";
license = licenses.lgpl3;
homepage = "http://snpeff.sourceforge.net/";
maintainers = with maintainers; [ jbedo ];
platforms = platforms.all;
};
}
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