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.

pkgs/applications/science/biology/rtg-tools/ant.patch

@@ -0,0 +1,21 @@
+--- ./build.xml.orig	2022-10-10 23:41:37.288306508 +0200
++++ ./build.xml	2022-10-10 23:43:22.316061657 +0200
+@@ -344,17 +344,10 @@
+     </javadoc>
+   </target>
+
+-  <scriptdef language="javascript" name="lowercase">
+-    <attribute name="value" />
+-    <attribute name="name" />
+-    project.setProperty(attributes.get("name"), attributes.get("value").toLowerCase());
+-  </scriptdef>
+-
+   <target name="zip-init" depends="rtg-vcs-info"> <!-- set up properties -->
+     <tstamp> <format property="build.tstamp" pattern="yyyyMMddHHmm" /></tstamp>
+     <propertyregex property="almostproductfilename" input="${product}" regexp="\s+" global="true" replace="-" />
+-    <property name="almostproductfilename" value="${product}" />
+-    <lowercase name="productfilename" value="${almostproductfilename}" />
++    <property name="productfilename" value="${product}" />
+     <condition property="zipversion"
+                value="${productfilename}-${product.version}"
+                else="${productfilename}-${product.version}-${rtg.vcs.commit.revision}">

pkgs/applications/science/biology/rtg-tools/default.nix

@@ -0,0 +1,49 @@
+{ config, lib, pkgs, 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=";
+  };
+
+  patches = [
+    ./ant.patch
+  ];
+
+  nativeBuildInputs = [
+    ant
+    jdk
+    git
+    unzip
+  ];
+
+  buildPhase = ''
+    ant rtg-tools.jar
+  '';
+
+  installPhase =''
+    mkdir -p $out/bin
+    cp build/rtg-tools.jar $out/bin/RTG.jar
+    cp installer/rtg $out/bin/
+  '';
+
+  fixupPhase = ''
+    # Use a location outside nix (must be writable)
+    sed -i 's|$THIS_DIR/rtg.cfg|$HOME/.rtg.cfg|g' $out/bin/rtg
+    # Use nix java
+    sed -i 's|RTG_JAVA="java".*|RTG_JAVA="${jdk}/lib/openjdk/bin/java"  # Nix Path to java|' $out/bin/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 ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -37406,6 +37406,8 @@ with pkgs;
 
   raxml-mpi = raxml.override { useMpi = true; };
 
+  rtg-tools = callPackage ../applications/science/biology/rtg-tools { };
+
   sambamba = callPackage ../applications/science/biology/sambamba { };
 
   samblaster = callPackage ../applications/science/biology/samblaster { };