picard-tools: init at 2.7.1

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

@@ -0,0 +1,30 @@
+{stdenv, fetchurl, jre, makeWrapper}:
+
+stdenv.mkDerivation rec {
+  name = "picard-tools-${version}";
+  version = "2.7.1";
+
+  src = fetchurl {
+    url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
+    sha256 = "0rcfcvy9zacqmh7nyqlm93hzsx6gfygmcf8d2p02h5l69gvygnb9";
+  };
+
+  buildInputs = [ jre makeWrapper ];
+
+  phases = [ "installPhase" ];
+
+  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 stdenv.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/;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.all;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -16998,6 +16998,8 @@ with pkgs;
 
   paml = callPackage ../applications/science/biology/paml { };
 
+  picard-tools = callPackage ../applications/science/biology/picard-tools/default.nix { };
+
   platypus = callPackage ../applications/science/biology/platypus/default.nix { };
 
   plink = callPackage ../applications/science/biology/plink/default.nix { };