fastqc: Initial packaging

pkgs/all-packages.nix

@@ -13,6 +13,8 @@ self: super: pkgs: with pkgs; {
 
   cryptominisat = callPackage ./cryptominisat.nix { python = python27; };
 
+  fastqc = callPackage ./fastqc.nix { };
+
   #firedrake = callPackage ./firedrake { };
 
   ghmm = callPackage ./ghmm { };

pkgs/fastqc.nix

@@ -0,0 +1,42 @@
+{ stdenv, fetchFromGitHub
+, jdk, ant, makeWrapper
+, jre, perl }:
+
+stdenv.mkDerivation rec {
+  name = "FastQC-${version}";
+  version = "0.11.8";
+  src = fetchFromGitHub {
+    name = "${name}-src";
+    owner = "s-andrews";
+    repo = "FastQC";
+    rev = "v${version}";
+    sha256 = "1xyf54ylvpv9kp110sf0hp1lqzx8plxh7a0k5yipggyqqhviv77j";
+  };
+
+  buildInputs = [ perl jdk ant makeWrapper ];
+
+  buildPhase = "ant";
+
+  installPhase = ''
+    install -d $out/share/FastQC $out/bin
+    install bin/fastqc $out/share/FastQC
+    cp -r bin/{Configuration,Help,Templates} $out/share/FastQC/
+    cp -r bin/{net,org,uk} $out/share/FastQC/
+    makeWrapper $out/share/FastQC/fastqc $out/bin/fastqc --add-flags --java=${jre}/bin/java
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://www.bioinformatics.babraham.ac.uk/projects/fastqc/;
+    description = "A quality control tool 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.
+    '';
+    platforms = platforms.all;
+    license = licenses.gpl23;
+  };
+}