Unverified Commit ca3bfcc5 authored by Gaétan Lepage's avatar Gaétan Lepage Committed by GitHub
Browse files

rtg-tools: fix path to core executables for hap.py. (#406276)

parents 9c8dbe3b 023b50d0

pkgs/by-name/rt/rtg-tools/package.nix

+12 −1
Original line number Diff line number Diff line
@@ -5,6 +5,9 @@ 
  jdk,

  ant,

  git,

  coreutils,

  hostname,

  gawk,

  unzip,

}:
@@ -44,11 +47,19 @@ stdenv.mkDerivation rec { 
    # 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"'

      --replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/opendk/bin/java"' \

      --replace-fail uname ${lib.getExe' coreutils "uname"} \

      --replace-fail awk ${lib.getExe gawk} \

      --replace-fail "hostname -s" "${lib.getExe hostname} -s"





    sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools'  installer/rtg

  '';



  checkPhase = ''

    ant runalltests

  '';



  meta = with lib; {

    homepage = "https://github.com/RealTimeGenomics/rtg-tools";

    description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";