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{ lib
, stdenvNoCC
, fetchFromGitHub
, jdk8
, jre8
, strip-nondeterminism
, makeWrapper
, zip
}:
let
jdk = jdk8;
jre = jre8;
in
stdenvNoCC.mkDerivation (finalAttrs: {
pname = "astral";
version = "5.7.1";
src = fetchFromGitHub {
owner = "smirarab";
repo = "ASTRAL";
rev = "v${finalAttrs.version}";
hash = "sha256-VhcsX9BxiZ0nISN6Xe4N+kq0iBMCtNhyxDrm9cwXfBA=";
};
patches = [
# we can't use stripJavaArchivesHook here, because the build process puts a .jar file into a zip file
# this patch calls strip-nondeterminism manually
./make-deterministic.patch
];
nativeBuildInputs = [
jdk
zip
strip-nondeterminism
makeWrapper
];
buildPhase = ''
runHook preBuild
patchShebangs ./make.sh
./make.sh
runHook postBuild
'';
doCheck = true;
checkPhase = ''
runHook preCheck
java -jar astral.${finalAttrs.version}.jar -i main/test_data/song_primates.424.gene.tre
runHook postCheck
'';
installPhase = ''
runHook preInstall
install -Dm644 astral.${finalAttrs.version}.jar -t $out/share
install -Dm644 lib/*.jar -t $out/share/lib
install -Dm644 Astral.${finalAttrs.version}.zip -t $out/share
cp -a main/test_data $out/share
makeWrapper ${jre}/bin/java $out/bin/astral \
--add-flags "-jar $out/share/astral.${finalAttrs.version}.jar"
runHook postInstall
'';
meta = with lib; {
homepage = "https://github.com/smirarab/ASTRAL";
description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees";
mainProgram = "astral";
sourceProvenance = with sourceTypes; [
fromSource
binaryBytecode # source bundles dependencies as jars
];
license = licenses.asl20;
maintainers = with maintainers; [ bzizou tomasajt ];
};
})
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