From 376897ced34becbfce58950225360c28e0a3ecf0 Mon Sep 17 00:00:00 2001
From: Bruno Bzeznik <Bruno.Bzeznik@imag.fr>
Date: Mon, 30 May 2022 14:53:28 +0200
Subject: [PATCH] astral: init at 5.7.1

---
 .../science/biology/astral/default.nix        | 56 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 58 insertions(+)
 create mode 100644 pkgs/applications/science/biology/astral/default.nix

diff --git a/pkgs/applications/science/biology/astral/default.nix b/pkgs/applications/science/biology/astral/default.nix
new file mode 100644
index 000000000000..b092edc0e602
--- /dev/null
+++ b/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 ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 97e824dbd049..56277e326a1a 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -32715,6 +32715,8 @@ with pkgs;
 
   aragorn = callPackage ../applications/science/biology/aragorn { };
 
+  astral = callPackage ../applications/science/biology/astral { };
+
   archimedes = callPackage ../applications/science/electronics/archimedes {
     stdenv = gcc6Stdenv;
   };