From 866fe591502ef2ce843d7568ffc3f48e3746110c Mon Sep 17 00:00:00 2001
From: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
Date: Tue, 20 Jul 2021 22:18:08 -0400
Subject: [PATCH] toil: init at 5.4.0

---
 .../science/misc/toil/default.nix             | 39 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 41 insertions(+)
 create mode 100644 pkgs/applications/science/misc/toil/default.nix

diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix
new file mode 100644
index 000000000000..bf3edab740db
--- /dev/null
+++ b/pkgs/applications/science/misc/toil/default.nix
@@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, python3Packages }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "toil";
+  version = "5.4.0";
+
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "docker = " "docker = 'docker' #" \
+      --replace "addict = " "addict = 'addict' #"
+  '';
+
+  propagatedBuildInputs = with python3Packages; [
+    addict
+    docker
+    pytz
+    pyyaml
+    enlighten
+    psutil
+    python-dateutil
+    dill
+  ];
+  checkInputs = with python3Packages; [ pytestCheckHook ];
+
+  pytestFlagsArray = [ "src/toil/test" ];
+  pythonImportsCheck = [ "toil" ];
+
+  meta = with lib; {
+    homepage = "http://toil.ucsc-cgl.org";
+    license = with licenses; [ asl20 ];
+    description = "Workflow engine written in pure Python";
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 44319d78c812..c4cac16ba29c 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -14349,6 +14349,8 @@ in
 
   todoist-electron = callPackage ../applications/misc/todoist-electron { };
 
+  toil = callPackage ../applications/science/misc/toil { };
+
   travis = callPackage ../development/tools/misc/travis { };
 
   tree-sitter = callPackage ../development/tools/parsing/tree-sitter {