From 5e775250ed44a569e14adc6828f1435ec615d8e0 Mon Sep 17 00:00:00 2001
From: David Crompton <davidcrompton1192@gmail.com>
Date: Thu, 25 May 2023 12:37:48 -0400
Subject: [PATCH] Numpy Override for Lumpy

---
 pkgs/all-packages.nix |  2 +-
 pkgs/lumpy.nix        | 24 ++++++++++++++++++++----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix
index 1776597..71ae4d1 100644
--- a/pkgs/all-packages.nix
+++ b/pkgs/all-packages.nix
@@ -11,7 +11,7 @@ final: prev: with prev; {
 
   gsort = callPackage ./gsort { };
 
-  lumpy = callPackage ./lumpy.nix { python=prev.python2; };
+  lumpy = callPackage ./lumpy.nix { };
 
   #meraculous = callPackage ./meraculous.nix { let stdenv49 = overrideCC stdenv gcc49; in stdenv = stdenv49; boost = boost159.override { stdenv = stdenv49 }; };
 
diff --git a/pkgs/lumpy.nix b/pkgs/lumpy.nix
index fc90d61..86758bb 100644
--- a/pkgs/lumpy.nix
+++ b/pkgs/lumpy.nix
@@ -1,8 +1,19 @@
 { stdenv, lib, fetchFromGitHub, which, autoconf, automake
 , zlib, curl
-, python, python2Packages, hexdump, sambamba, samblaster, samtools }:
-
-stdenv.mkDerivation rec {
+, python2, hexdump, sambamba, samblaster, samtools }: let
+  python = python2.override {
+    packageOverrides = final: prev: {
+      numpy = prev.numpy.overridePythonAttrs(old: rec {
+        version = "1.16.6";
+        src = fetchPypi {
+          inherit pname version;
+          extension = "zip";
+          sha256 = "e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff";
+        };
+      });
+    };
+  };
+in stdenv.mkDerivation rec {
   version = "0.3.0";
   name = "lumpy-${version}";
 
@@ -39,7 +50,12 @@ stdenv.mkDerivation rec {
     automake
     zlib
     curl
-    (python.withPackages (packages: with packages; [ numpy pysam ]))
+    (python.withPackages (packages: with packages;
+      [
+        numpy
+        pysam
+      ]
+    ))
     hexdump
     sambamba
     samblaster