1 files changed, 33 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
new file mode 100644
index 000000000000..880ea77e9d24
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -0,0 +1,33 @@
+{lib, stdenv, fetchurl, jre, makeWrapper}:
+
+stdenv.mkDerivation rec {
+  pname = "picard-tools";
+  version = "3.1.1";
+
+  src = fetchurl {
+    url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
+    sha256 = "sha256-FcefUf0KwAEEn53XubrB2991ncsCMKicf20fJG6LurQ=";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
+
+  dontUnpack = true;
+
+  installPhase = ''
+    mkdir -p $out/libexec/picard
+    cp $src $out/libexec/picard/picard.jar
+    mkdir -p $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar"
+  '';
+
+  meta = with lib; {
+    description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
+    license = licenses.mit;
+    homepage = "https://broadinstitute.github.io/picard/";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    maintainers = with maintainers; [ jbedo ];
+    mainProgram = "picard";
+    platforms = platforms.all;
+  };
+}