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{ 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 ];
};
}
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