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