From 4b3112f8a4798470e5896670e6f7536eae01337e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 15:09:56 +1100
Subject: [PATCH] pythonPackages.bx-python: init at 0.8.6

---
 .../python-modules/bx-python/default.nix      | 39 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  4 ++
 2 files changed, 43 insertions(+)
 create mode 100644 pkgs/development/python-modules/bx-python/default.nix

diff --git a/pkgs/development/python-modules/bx-python/default.nix b/pkgs/development/python-modules/bx-python/default.nix
new file mode 100644
index 000000000000..57a3609bad0a
--- /dev/null
+++ b/pkgs/development/python-modules/bx-python/default.nix
@@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, buildPythonPackage, isPy27, numpy, cython, zlib, six
+, python-lzo, nose }:
+
+buildPythonPackage rec {
+  pname = "bx-python";
+  version = "0.8.6";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "bxlab";
+    repo = "bx-python";
+    rev = "v${version}";
+    sha256 = "1i40vmn8n83vqcpqj843riv9vp16s753jc4wc90p0cmrnhmzcv13";
+  };
+
+  nativeBuildInputs = [ cython ];
+  buildInputs = [ zlib ];
+  propagatedBuildInputs = [ numpy six python-lzo ];
+  checkInputs = [ nose ];
+
+  postInstall = ''
+    cp -r scripts/* $out/bin
+
+    # This is a small hack; the test suit uses the scripts which need to
+    # be patched. Linking the patched scripts in $out back to the
+    # working directory allows the tests to run
+    rm -rf scripts
+    ln -s $out/bin scripts
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/bxlab/bx-python";
+    description =
+      "Tools for manipulating biological data, particularly multiple sequence alignments";
+    license = licenses.mit;
+    maintainers = [ maintainers.jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 42c885c29295..4da1aeba98db 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1694,6 +1694,10 @@ in {
 
   bumps = callPackage ../development/python-modules/bumps {};
 
+  bx-python = callPackage ../development/python-modules/bx-python {
+    inherit (pkgs) zlib;
+  };
+
   cached-property = callPackage ../development/python-modules/cached-property { };
 
   caffe = toPythonModule (pkgs.caffe.override {