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{ lib
, stdenv
, fetchFromGitHub
, ant
, jdk
, jre
, makeWrapper
, stripJavaArchivesHook
}:
stdenv.mkDerivation (finalAttrs: {
pname = "trimmomatic";
version = "0.39";
src = fetchFromGitHub {
owner = "usadellab";
repo = "Trimmomatic";
rev = "v${finalAttrs.version}";
hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I=";
};
# Remove jdk version requirement
postPatch = ''
substituteInPlace ./build.xml \
--replace 'source="1.5" target="1.5"' ""
'';
nativeBuildInputs = [
ant
jdk
makeWrapper
stripJavaArchivesHook
];
buildPhase = ''
runHook preBuild
ant
runHook postBuild
'';
installPhase = ''
runHook preInstall
install -Dm644 dist/jar/trimmomatic-*.jar -t $out/share/trimmomatic
cp -r adapters $out/share/trimmomatic
makeWrapper ${jre}/bin/java $out/bin/trimmomatic \
--add-flags "-jar $out/share/trimmomatic/trimmomatic-*.jar"
runHook postInstall
'';
meta = {
changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt";
description = "A flexible read trimming tool for Illumina NGS data";
longDescription = ''
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data: adapter trimming, quality trimming,
cropping to a specified length, length filtering, quality score
conversion.
'';
homepage = "http://www.usadellab.org/cms/?page=trimmomatic";
downloadPage = "https://github.com/usadellab/Trimmomatic/releases";
license = lib.licenses.gpl3Only;
sourceProvenance = [
lib.sourceTypes.fromSource
lib.sourceTypes.binaryBytecode # source bundles dependencies as jars
];
mainProgram = "trimmomatic";
maintainers = [ lib.maintainers.kupac ];
};
})
|