65 lines
1.7 KiB
Nix
65 lines
1.7 KiB
Nix
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{
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lib,
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fetchFromGitHub,
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jre_minimal,
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makeWrapper,
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stripJavaArchivesHook,
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maven,
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nix-update-script,
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}:
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maven.buildMavenPackage rec {
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pname = "trimmomatic";
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version = "0.40";
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src = fetchFromGitHub {
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owner = "usadellab";
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repo = "Trimmomatic";
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rev = "v${version}";
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hash = "sha256-pLUjSVePN++G2XZrdKEdobgBO+UD0PZ9wlhSUlZ7na8=";
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};
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mvnHash = "sha256-1XnVdud8nI2SuEPXnwEmbudM+QAeoSVTn0UZ8PKJH44=";
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nativeBuildInputs = [
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makeWrapper
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stripJavaArchivesHook
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];
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installPhase = ''
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runHook preInstall
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install -Dm644 target/trimmomatic-${version}.jar -t $out/share/trimmomatic
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cp -r adapters $out/share/trimmomatic
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makeWrapper ${lib.getBin jre_minimal}/bin/java $out/bin/trimmomatic \
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--add-flags "-jar $out/share/trimmomatic/trimmomatic-${version}.jar"
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runHook postInstall
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'';
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passthru = {
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updateScript = nix-update-script { };
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};
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meta = {
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changelog = "https://github.com/usadellab/Trimmomatic/releases/tag/v${version}";
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description = "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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mainProgram = "trimmomatic";
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maintainers = [ lib.maintainers.kupac ];
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};
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}
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