From 5859c5b472d68155c4c91767b5892f347a1a2e89 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Jun 2019 13:20:19 +1000
Subject: [PATCH 1/3] pythonPackages.pomegranate: 0.8.1 -> 0.11.0

---
 .../python-modules/pomegranate/default.nix         | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/pomegranate/default.nix b/pkgs/development/python-modules/pomegranate/default.nix
index e611e2ea5b1..7054485f302 100644
--- a/pkgs/development/python-modules/pomegranate/default.nix
+++ b/pkgs/development/python-modules/pomegranate/default.nix
@@ -1,17 +1,17 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, cython, networkx, joblib, nose }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, cython, networkx, joblib, nose, pyyaml }:
 
 buildPythonPackage rec {
   pname = "pomegranate";
-  version = "0.8.1";
-  
+  version = "0.11.0";
+
   src = fetchFromGitHub {
     repo = pname;
     owner = "jmschrei";
     rev = "v${version}";
-    sha256 = "085nka5bh88bxbd5vl1azyv9cfpp6grz2ngclc85f9kgccac1djr";
+    sha256 = "0gf7z343ag4g7pfccn1sdap3ihkaxrc9ca75awjhmsa2cyqs66df";
   };
 
-  propagatedBuildInputs = [ numpy scipy cython networkx joblib ];
+  propagatedBuildInputs = [ numpy scipy cython networkx joblib pyyaml ];
 
   checkInputs = [ nose ];
 
@@ -20,9 +20,5 @@ buildPythonPackage rec {
     homepage = https://github.com/jmschrei/pomegranate;
     license = licenses.mit;
     maintainers = with maintainers; [ rybern ];
-
-    # "pomegranate does not yet work with networkx 2.0"
-    # see https://github.com/jmschrei/pomegranate/issues/209
-    broken = true; 
   };
 }

From 4bb197f4b26ac81b9d37700fc0caaa6d3cdab0b2 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 5 Jul 2019 15:04:17 +1000
Subject: [PATCH 2/3] pythonPackages.pyfaidx: init at 0.5.5.2

---
 .../python-modules/pyfaidx/default.nix        | 24 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 26 insertions(+)
 create mode 100644 pkgs/development/python-modules/pyfaidx/default.nix

diff --git a/pkgs/development/python-modules/pyfaidx/default.nix b/pkgs/development/python-modules/pyfaidx/default.nix
new file mode 100644
index 00000000000..26c36e70d0c
--- /dev/null
+++ b/pkgs/development/python-modules/pyfaidx/default.nix
@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "pyfaidx";
+  version = "0.5.5.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1akc8hk8rlw7sv07bv1n2r471acvmxwc57gb69frjpcwggf2phls";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  meta = with lib; {
+    homepage = "https://github.com/mdshw5/pyfaidx";
+    description = "Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.jbedo ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index d927073d72e..1728b4bece4 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -722,6 +722,8 @@ in {
 
   pyfakefs = callPackage ../development/python-modules/pyfakefs {};
 
+  pyfaidx = callPackage ../development/python-modules/pyfaidx { };
+
   pyfttt = callPackage ../development/python-modules/pyfttt { };
 
   pyftdi = callPackage ../development/python-modules/pyftdi { };

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 3/3] 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 { };