varscan: init at 2.4.2

pkgs/applications/science/biology/varscan/default.nix

@@ -0,0 +1,36 @@
+{stdenv, fetchurl, jre, makeWrapper}:
+
+stdenv.mkDerivation rec {
+  name = "varscan-${version}";
+  version = "2.4.2";
+
+  src = fetchurl {
+    url = "https://github.com/dkoboldt/varscan/releases/download/${version}/VarScan.v${version}.jar";
+    sha256 = "0cfhshinyqgwc6i7zf8lhbfybyly2x5anrz824zyvdhzz5i69zrl";
+  };
+
+  buildInputs = [ jre makeWrapper ];
+
+  phases = [ "installPhase" ];
+
+  installPhase = ''
+    mkdir -p $out/libexec/varscan
+    cp $src $out/libexec/varscan/varscan.jar
+    mkdir -p $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data";
+    # VarScan 2 is free for non-commercial use by academic,
+    # government, and non-profit/not-for-profit institutions. A
+    # commercial version of the software is available, and licensed
+    # through the Office of Technology Management at Washington
+    # University School of Medicine.
+    license = licenses.unfree;
+    homepage = https://github.com/dkoboldt/varscan;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.all;
+  };
+
+}

pkgs/top-level/all-packages.nix

@@ -17008,6 +17008,8 @@ with pkgs;
 
   samtools = callPackage ../applications/science/biology/samtools/default.nix { };
 
+  varscan = callPackage ../applications/science/biology/varscan/default.nix { };
+
   bwa = callPackage ../applications/science/biology/bwa/default.nix { };
 
   ### SCIENCE/MATH