diff options
author | Alexis Praga <alexis.praga@free.fr> | 2023-05-06 22:32:52 +0200 |
---|---|---|
committer | Alexis Praga <alexis.praga@proton.me> | 2024-04-02 23:20:30 +0200 |
commit | 7629ea877f832c3e91b1e5014409bc3ab4cc4c65 (patch) | |
tree | 060926f8b3b7393fc54592939e154cb88465d30c | |
parent | 76fd5b7e0a831f29cbdc333417cf315d77467234 (diff) |
rtg-tools: init at 3.12.1
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.
-rw-r--r-- | pkgs/by-name/rt/rtg-tools/package.nix | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/pkgs/by-name/rt/rtg-tools/package.nix b/pkgs/by-name/rt/rtg-tools/package.nix new file mode 100644 index 0000000000000..7872df77e61b0 --- /dev/null +++ b/pkgs/by-name/rt/rtg-tools/package.nix @@ -0,0 +1,59 @@ +{ + lib, + stdenv, + fetchFromGitHub, + jdk, + ant, + git, + unzip, +}: + +stdenv.mkDerivation rec { + pname = "rtg-tools"; + version = "3.12.1"; + + src = fetchFromGitHub { + owner = "RealTimeGenomics"; + repo = "rtg-tools"; + rev = version; + sha256 = "sha256-fMrrjrgaGxBVxn6qMq2g0oFv6qtfhZcQlkvv1E9Os6Y="; + }; + + nativeBuildInputs = [ + ant + jdk + git # Required by build.xml to manage the build revision + unzip + ]; + + buildPhase = '' + runHook preBuild + ant rtg-tools.jar + runHook postBuild + ''; + + installPhase = '' + runHook preInstall + mkdir -p $out/bin + cp build/rtg-tools.jar $out/bin/RTG.jar + cp installer/rtg $out/bin/ + runHook postInstall + ''; + + postPatch = '' + # Use a location outside nix (must be writable) + substituteInPlace installer/rtg \ + --replace-fail '$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 + ''; + + 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 ]; + }; +} |