From 91e6ec3f53b9183082f56c0e52931436d069528e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 26 Sep 2018 11:24:18 +1000
Subject: Add flagstat and fastqc

---
 tools/fastqc-app.nix | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 tools/fastqc-app.nix

(limited to 'tools/fastqc-app.nix')

diff --git a/tools/fastqc-app.nix b/tools/fastqc-app.nix
new file mode 100644
index 0000000..40fd7ec
--- /dev/null
+++ b/tools/fastqc-app.nix
@@ -0,0 +1,24 @@
+{ stdenv, unzip, perl, fetchurl, jre }:
+
+stdenv.mkDerivation rec {
+  name = "fastqc-${version}";
+  version = "0.11.7";
+
+  src = fetchurl {
+    url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip";
+    sha256 = "04hifbfrh60s5kzqr7n46bcviaiymr1rx67b88s3cpxydf3m1ksr";
+  };
+
+  buildInputs = [ unzip perl ];
+
+  phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
+
+  installPhase = ''
+    mkdir -p $out/libexec/fastqc
+    cp -r . $out/libexec/fastqc
+    mkdir $out/bin
+    ln -s $out/libexec/fastqc/fastqc $out/bin
+    substituteInPlace $out/bin/fastqc --replace "my \$java_bin = 'java'" "my \$java_bin = '${jre}/bin/java'"
+    chmod 755 $out/libexec/fastqc/fastqc
+  '';
+}
-- 
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