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{stdenv, fetchurl, jre, makeWrapper}:
stdenv.mkDerivation rec {
pname = "picard-tools";
version = "2.22.0";
src = fetchurl {
url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
sha256 = "1qgg8r81xn2z965v78kfj05vycrd2cz48gxk5csr6kvwk3ba286c";
};
nativeBuildInputs = [ makeWrapper ];
buildInputs = [ jre ];
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";
license = licenses.mit;
homepage = "https://broadinstitute.github.io/picard/";
maintainers = with maintainers; [ jbedo ];
platforms = platforms.all;
};
}
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