646b892680
Some checks failed
Periodic Merges (6h) / master → staging-nixos (push) Failing after 12m50s
Periodic Merges (6h) / master → staging-next (push) Failing after 12m54s
Periodic Merges (24h) / merge-base(master,staging) → haskell-updates (push) Failing after 11m54s
Periodic Merges (6h) / staging-next → staging (push) Failing after 12m13s
Periodic Merges (24h) / staging-next-25.05 → staging-25.05 (push) Failing after 13m24s
Periodic Merges (24h) / release-25.05 → staging-next-25.05 (push) Failing after 14m28s
84 lines
1.8 KiB
Nix
84 lines
1.8 KiB
Nix
{
|
|
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
|
|
];
|
|
};
|
|
})
|