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nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix

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{stdenv, fetchurl, jre, makeWrapper}:
stdenv.mkDerivation rec {
name = "picard-tools-${version}";
version = "2.18.17";
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src = fetchurl {
url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
sha256 = "0ks7ymrjfya5h77hp0bqyipzdri0kf97c8wks32nvwkj821687zm";
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};
nativeBuildInputs = [ makeWrapper ];
buildInputs = [ jre ];
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phases = [ "installPhase" ];
installPhase = ''
mkdir -p $out/libexec/picard
cp $src $out/libexec/picard/picard.jar
mkdir -p $out/bin
makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar"
'';
meta = with stdenv.lib; {
description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
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license = licenses.mit;
homepage = https://broadinstitute.github.io/picard/;
maintainers = with maintainers; [ jbedo ];
platforms = platforms.all;
};
}