From f889214bc16470126095ca1c292fb64ec467bb9f Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Jun 2019 13:26:26 +1000
Subject: [PATCH] pythonPackages.cnvkit: init at 0.9.6

---
 .../python-modules/cnvkit/default.nix         | 48 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 50 insertions(+)
 create mode 100644 pkgs/development/python-modules/cnvkit/default.nix

diff --git a/pkgs/development/python-modules/cnvkit/default.nix b/pkgs/development/python-modules/cnvkit/default.nix
new file mode 100644
index 00000000000..905b274a055
--- /dev/null
+++ b/pkgs/development/python-modules/cnvkit/default.nix
@@ -0,0 +1,48 @@
+{ lib
+, fetchPypi
+, rPackages
+, rWrapper
+, buildPythonPackage
+, biopython
+, numpy
+, scipy
+, pandas
+, matplotlib
+, reportlab
+, pysam
+, future
+, pillow
+, pomegranate
+, pyfaidx
+}:
+
+buildPythonPackage rec {
+  pname = "CNVkit";
+  version = "0.9.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hj8c98s538i0hg5mrz4bw4v07qmcl51rhxq611rj2nglnc9r25y";
+  };
+
+  propagatedBuildInputs = [
+    biopython
+    numpy
+    scipy
+    pandas
+    matplotlib
+    reportlab
+    pyfaidx
+    pysam
+    future
+    pillow
+    pomegranate
+  ];
+
+  meta = with lib; {
+    homepage = "https://cnvkit.readthedocs.io";
+    description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
+    license = licenses.asl20;
+    maintainers = [ maintainers.jbedo ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 1728b4bece4..584ffe6c86e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -346,6 +346,8 @@ in {
 
   clustershell = callPackage ../development/python-modules/clustershell { };
 
+  cnvkit = callPackage ../development/python-modules/cnvkit { };
+
   cozy = callPackage ../development/python-modules/cozy { };
 
   curio = callPackage ../development/python-modules/curio { };