67 lines
1.7 KiB
Nix
67 lines
1.7 KiB
Nix
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{ lib
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, stdenv
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, ant
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, fetchFromGitHub
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, jdk11_headless
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, jre
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, makeWrapper
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}:
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stdenv.mkDerivation rec {
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pname = "trimmomatic";
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version = "0.39";
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src = fetchFromGitHub {
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owner = "usadellab";
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repo = "Trimmomatic";
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rev = "v${version}";
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hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";
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};
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# Set source and target version to 11
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postPatch = ''
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substituteInPlace ./build.xml \
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--replace 'source="1.5" target="1.5"' 'release="11"'
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'';
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nativeBuildInputs = [ jdk11_headless ant makeWrapper ];
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buildPhase = ''
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runHook preBuild
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ant
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runHook postBuild
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'';
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin $out/share
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cp dist/jar/trimmomatic-${version}.jar $out/share/
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cp -r adapters $out/share/
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makeWrapper ${jre}/bin/java $out/bin/trimmomatic \
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--add-flags "-cp $out/share/trimmomatic-${version}.jar org.usadellab.trimmomatic.Trimmomatic"
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runHook postInstall
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'';
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meta = {
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description = "A flexible read trimming tool for Illumina NGS data";
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longDescription = ''
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Trimmomatic performs a variety of useful trimming tasks for illumina
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paired-end and single ended data: adapter trimming, quality trimming,
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cropping to a specified length, length filtering, quality score
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conversion.
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'';
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homepage = "http://www.usadellab.org/cms/?page=trimmomatic";
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downloadPage = "https://github.com/usadellab/Trimmomatic/releases";
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license = lib.licenses.gpl3Only;
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sourceProvenance = [
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lib.sourceTypes.fromSource
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lib.sourceTypes.binaryBytecode # source bundles dependencies as jars
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];
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maintainers = [ lib.maintainers.kupac ];
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};
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}
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