Merge pull request #175477 from bzizou/astral

astral: init at 5.7.1

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

@@ -0,0 +1,56 @@
+{ lib
+, stdenvNoCC
+, fetchFromGitHub
+, jdk8
+, makeWrapper
+, jre8
+, zip
+}:
+let
+  jdk = jdk8;
+  jre = jre8;
+in
+stdenvNoCC.mkDerivation rec {
+  pname = "astral";
+  version = "5.7.1";
+
+  src = fetchFromGitHub {
+    owner = "smirarab";
+    repo = "ASTRAL";
+    rev = "v${version}";
+    sha256 = "043w2z6gbrisqirdid022f4b8jps1pp5syi344krv2bis1gjq5sn";
+  };
+
+  nativeBuildInputs = [ jdk makeWrapper jre zip ];
+
+  buildPhase = ''
+    patchShebangs ./make.sh
+    ./make.sh
+  '';
+
+  doCheck = true;
+
+  checkPhase = ''
+    runHook preCheck
+    java -jar astral.${version}.jar -i main/test_data/song_primates.424.gene.tre
+    runHook postCheck
+  '';
+
+  installPhase = ''
+    mkdir -p $out/share/lib
+    mkdir -p $out/bin
+    mv astral.${version}.jar $out/share/
+    mv lib/*.jar $out/share/lib
+    mv Astral.${version}.zip $out/share/
+    cp -a  main/test_data $out/share/
+    makeWrapper ${jre}/bin/java $out/bin/astral \
+        --add-flags "-jar $out/share/astral.${version}.jar"
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/smirarab/ASTRAL";
+    description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ bzizou ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -32732,6 +32732,8 @@ with pkgs;
 
   aragorn = callPackage ../applications/science/biology/aragorn { };
 
+  astral = callPackage ../applications/science/biology/astral { };
+
   archimedes = callPackage ../applications/science/electronics/archimedes {
     stdenv = gcc6Stdenv;
   };