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