From db8655693e03920634c7b73bb37122864f2a954e Mon Sep 17 00:00:00 2001
From: Tyson Whitehead <twhitehead@gmail.com>
Date: Tue, 25 Jun 2019 11:56:13 -0400
Subject: [PATCH] cutadapt: Initial packaging

---
 pkgs/cutadapt.nix        | 25 +++++++++++++++++++++++++
 pkgs/python-packages.nix |  2 ++
 2 files changed, 27 insertions(+)
 create mode 100644 pkgs/cutadapt.nix

diff --git a/pkgs/cutadapt.nix b/pkgs/cutadapt.nix
new file mode 100644
index 0000000..777e7e0
--- /dev/null
+++ b/pkgs/cutadapt.nix
@@ -0,0 +1,25 @@
+{ lib, fetchPypi, buildPythonPackage, isPy3k
+, cython, setuptools_scm
+, dnaio, xopen, pytest, pytest-timeout, sphinx }:
+
+buildPythonPackage rec {
+  version = "2.3";
+  pname = "cutadapt";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1b4jdq565vwx44azjj7gsaszckzxbgnakpbvi5im4ll1knn69f4q";
+  };
+
+  disabled = !isPy3k;
+
+  buildInputs = [ cython setuptools_scm ];
+  propagatedBuildInputs = [ dnaio xopen ];
+  checkInputs = [ pytest pytest-timeout sphinx ];
+
+  meta = with lib; {
+    homepage = "https://cutadapt.readthedocs.io";
+    description = "Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.";
+    license = licenses.mit;
+  };
+}
diff --git a/pkgs/python-packages.nix b/pkgs/python-packages.nix
index 376173a..e40f71f 100644
--- a/pkgs/python-packages.nix
+++ b/pkgs/python-packages.nix
@@ -1,5 +1,7 @@
 pkgs: self: super: with self; {
 
+  cutadapt = callPackage ./cutadapt.nix { };
+
   dnaio = callPackage ./dnaio.nix { };
 
   ghmm = disabledIf isPy3k ( toPythonModule (pkgs.ghmm.override { python2Packages=self; }) ).py;