From 00af52229ec39be87e7633db7f2dbc090adc3dff Mon Sep 17 00:00:00 2001
From: David Flores <david.flores@ucm.es>
Date: Sun, 10 Mar 2024 23:43:32 +0100
Subject: [PATCH] fastqc: init at 0.12.1

fastqc: remove trailing whitespaces

fastqc: moved to by-name hierarchy

Update pkgs/by-name/fa/fastqc/package.nix

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

Update pkgs/by-name/fa/fastqc/package.nix

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

Update pkgs/by-name/fa/fastqc/package.nix

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

Update pkgs/by-name/fa/fastqc/package.nix

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

Update pkgs/by-name/fa/fastqc/package.nix

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

fastqc: suggested code changes applied

fastqc: added testVersion

fastqc: some corrections

fastqc: remove with lib;
---
 pkgs/by-name/fa/fastqc/package.nix | 83 ++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 pkgs/by-name/fa/fastqc/package.nix

diff --git a/pkgs/by-name/fa/fastqc/package.nix b/pkgs/by-name/fa/fastqc/package.nix
new file mode 100644
index 000000000000..e7973ab0d602
--- /dev/null
+++ b/pkgs/by-name/fa/fastqc/package.nix
@@ -0,0 +1,83 @@
+{ 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.isLinux copyDesktopItems # postInstallHook
+                      ++ lib.optional stdenv.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;
+  };
+})