7629ea877f
A subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Mostly used for vcfeval to compare VCF.
60 lines
1.3 KiB
Nix
60 lines
1.3 KiB
Nix
{
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lib,
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stdenv,
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fetchFromGitHub,
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jdk,
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ant,
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git,
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unzip,
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}:
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stdenv.mkDerivation rec {
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pname = "rtg-tools";
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version = "3.12.1";
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src = fetchFromGitHub {
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owner = "RealTimeGenomics";
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repo = "rtg-tools";
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rev = version;
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sha256 = "sha256-fMrrjrgaGxBVxn6qMq2g0oFv6qtfhZcQlkvv1E9Os6Y=";
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};
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nativeBuildInputs = [
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ant
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jdk
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git # Required by build.xml to manage the build revision
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unzip
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];
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buildPhase = ''
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runHook preBuild
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ant rtg-tools.jar
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runHook postBuild
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'';
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin
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cp build/rtg-tools.jar $out/bin/RTG.jar
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cp installer/rtg $out/bin/
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runHook postInstall
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'';
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postPatch = ''
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# Use a location outside nix (must be writable)
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substituteInPlace installer/rtg \
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--replace-fail '$THIS_DIR/rtg.cfg' '$HOME/.config/rtg-tools/rtg.cfg' \
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--replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/openjdk/bin/java"'
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sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools' installer/rtg
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'';
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meta = with lib; {
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homepage = "https://github.com/RealTimeGenomics/rtg-tools";
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description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";
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license = licenses.bsd2;
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platforms = [ "x86_64-linux" ];
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maintainers = with maintainers; [ apraga ];
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};
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}
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