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2e6bf42a22
There ver very many conflicts, basically all due to name -> pname+version. Fortunately, almost everything was auto-resolved by kdiff3, and for now I just fixed up a couple evaluation problems, as verified by the tarball job. There might be some fallback to these conflicts, but I believe it should be minimal. Hydra nixpkgs: ?compare=1538299
32 lines
930 B
Nix
32 lines
930 B
Nix
{stdenv, fetchurl, jre, makeWrapper}:
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stdenv.mkDerivation rec {
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pname = "picard-tools";
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version = "2.20.5";
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src = fetchurl {
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url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
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sha256 = "107zlvp74ahpn652nfkipp80bbzf3fp812pi1ma42njk4wchah10";
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};
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nativeBuildInputs = [ makeWrapper ];
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buildInputs = [ jre ];
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phases = [ "installPhase" ];
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installPhase = ''
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mkdir -p $out/libexec/picard
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cp $src $out/libexec/picard/picard.jar
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mkdir -p $out/bin
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makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar"
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'';
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meta = with stdenv.lib; {
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description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
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license = licenses.mit;
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homepage = https://broadinstitute.github.io/picard/;
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maintainers = with maintainers; [ jbedo ];
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platforms = platforms.all;
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};
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}
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