From 076e513b94a4bd42c635394c393fb583f9dbadc3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 7 Mar 2017 16:24:06 +1100
Subject: [PATCH] varscan: init at 2.4.2

---
 .../science/biology/varscan/default.nix       | 36 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 38 insertions(+)
 create mode 100644 pkgs/applications/science/biology/varscan/default.nix

diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix
new file mode 100644
index 000000000000..f685031e87e4
--- /dev/null
+++ b/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;
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 47e75c8632a2..d59650440477 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/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