From a141544cb5877dbb35959cb04cf48aa89ef45ef1 Mon Sep 17 00:00:00 2001
From: Robert Djubek <envy1988@gmail.com>
Date: Thu, 14 Mar 2019 03:15:09 +0000
Subject: [PATCH] pythonPackages.ruffus: init at 2.8.1

---
 .../python-modules/ruffus/default.nix         | 53 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 55 insertions(+)
 create mode 100644 pkgs/development/python-modules/ruffus/default.nix

diff --git a/pkgs/development/python-modules/ruffus/default.nix b/pkgs/development/python-modules/ruffus/default.nix
new file mode 100644
index 00000000000..1b3b271fb61
--- /dev/null
+++ b/pkgs/development/python-modules/ruffus/default.nix
@@ -0,0 +1,53 @@
+{ gevent
+, buildPythonPackage
+, fetchFromGitHub
+, hostname
+, pytest
+, python
+, stdenv
+}:
+
+buildPythonPackage rec {
+  pname = "ruffus";
+  version = "2.8.1";
+
+  src = fetchFromGitHub {
+    owner = "cgat-developers";
+    repo = "${pname}";
+    rev = "v${version}";
+    sha256 = "1gyabqafq4s2sy0prh3k1m8859shzjmfxr7fimx10liflvki96a9";
+  };
+
+  propagatedBuildInputs = [ gevent ];
+
+  postPatch = ''
+    sed -i -e 's|/bin/bash|${stdenv.shell}|'          ruffus/test/Makefile
+    sed -i -e 's|\tpytest|\t${pytest}/bin/pytest|'    ruffus/test/Makefile
+    sed -i -e 's|\tpython|\t${python.interpreter}|'   ruffus/test/Makefile
+    sed -i -e 's|/usr/bin/env bash|${stdenv.shell}|'  ruffus/test/run_all_unit_tests.cmd
+    sed -i -e 's|python3|${python.interpreter}|'      ruffus/test/run_all_unit_tests3.cmd
+    sed -i -e 's|python %s|${python.interpreter} %s|' ruffus/test/test_drmaa_wrapper_run_job_locally.py
+  '';
+
+  makefile = "ruffus/test/Makefile";
+
+  checkInputs = [
+    gevent
+    hostname
+    pytest
+  ];
+
+  checkPhase = ''
+    export HOME=$TMPDIR
+    cd ruffus/test
+    make all PYTEST_OPTIONS="-q --disable-warnings"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Light-weight Python Computational Pipeline Management";
+    homepage = http://www.ruffus.org.uk;
+    license = licenses.mit;
+    maintainers = [ maintainers.kiwi ];
+  };
+}
+
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index d6b092d8bdb..1c0322e2d15 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5057,6 +5057,8 @@ in {
 
   ruamel_yaml = callPackage ../development/python-modules/ruamel_yaml { };
 
+  ruffus = callPackage ../development/python-modules/ruffus { };
+
   runsnakerun = callPackage ../development/python-modules/runsnakerun { };
 
   pysendfile = callPackage ../development/python-modules/pysendfile { };