70 lines
1.6 KiB
Nix
70 lines
1.6 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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coreutils,
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hostname,
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gawk,
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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 = "3.13";
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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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hash = "sha256-vPzKrgnX6BCQmn9aOVWWpFLC6SbPBHZhZ+oL1LCbvmo=";
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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' '$HOME/.config/rtg-tools/rtg.cfg' \
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--replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${lib.getExe jdk}"' \
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--replace-fail uname ${lib.getExe' coreutils "uname"} \
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--replace-fail awk ${lib.getExe gawk} \
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--replace-fail "hostname -s" "${lib.getExe hostname} -s"
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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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checkPhase = ''
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ant runalltests
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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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