Add flagstat and fastqc

1 files changed, 24 insertions, 0 deletions

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
+  '';
+}