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{ lib,
stdenv,
fetchzip,
jre,
perl,
makeWrapper,
imagemagick,
makeDesktopItem,
copyDesktopItems,
desktopToDarwinBundle,
testers
}:
stdenv.mkDerivation (finalAttrs: {
pname = "fastqc";
version = "0.12.1";
src = fetchzip {
url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${finalAttrs.version}.zip";
hash = "sha256-TenRG2x8ivJ2HM2ZpLaJShp0yI0Qc6K5lW5/NJFAa1I";
};
dontBuild = true;
nativeBuildInputs = [ makeWrapper imagemagick ]
++ lib.optional stdenv.hostPlatform.isLinux copyDesktopItems # postInstallHook
++ lib.optional stdenv.hostPlatform.isDarwin desktopToDarwinBundle; #fixupOutputHook
buildInputs = [ jre perl];
desktopItem = (makeDesktopItem {
name = "FastQC";
exec = "fastqc";
icon = "fastqc";
desktopName = "FastQC";
comment = finalAttrs.meta.description;
categories = [ "Science" ];
});
desktopItems = [ finalAttrs.desktopItem ];
installPhase = ''
runHook preInstall
mkdir -p $out/{bin,FastQC}
cp -r $src/* $out/FastQC
# Create desktop item
mkdir -p $out/share/{applications,icons}
# Freedesktop doesn't support windows ICO files. Use imagemagick to convert it to PNG
convert $out/FastQC/fastqc_icon.ico $out/share/icons/fastqc.png
runHook postInstall
'';
preFixup = ''
makeWrapper $out/FastQC/fastqc $out/bin/fastqc --prefix PATH : ${jre}/bin
'';
passthru.tests.version = testers.testVersion {
package = finalAttrs.finalPackage;
version = "v${finalAttrs.version}";
};
meta = {
description = "A quality control application for high throughput sequence data";
longDescription = ''
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
The main functions of FastQC are
- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application
'';
homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/";
sourceProvenance = [ lib.sourceTypes.binaryNativeCode ];
license = with lib.licenses; [ gpl3Plus asl20 ];
maintainers = [ lib.maintainers.dflores ];
mainProgram = "fastqc";
platforms = lib.platforms.unix;
};
})
|
