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571c71e6f7
We are migrating packages that meet below requirements:
1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration
The tool is here: https://github.com/Aleksanaa/by-name-migrate.
34 lines
1007 B
Nix
34 lines
1007 B
Nix
{lib, stdenv, fetchurl, jre, makeWrapper}:
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stdenv.mkDerivation rec {
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pname = "picard-tools";
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version = "3.3.0";
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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 = "sha256-WIGadmBka3SzTigvXU0hyNuuoi3e/5bjJYdV2voPhtw=";
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};
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nativeBuildInputs = [ makeWrapper ];
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buildInputs = [ jre ];
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dontUnpack = true;
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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 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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sourceProvenance = with sourceTypes; [ binaryBytecode ];
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maintainers = with maintainers; [ jbedo ];
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mainProgram = "picard";
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platforms = platforms.all;
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};
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}
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