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

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

@@ -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";