From 05a704f9890a50fac93208fd7b5f3e006ebf1b2a Mon Sep 17 00:00:00 2001
From: Tyson Whitehead <twhitehead@gmail.com>
Date: Wed, 30 Oct 2019 13:07:39 -0400
Subject: [PATCH] lumpy: bamkit python files should be in bamkit subdirectory

---
 pkgs/lumpy.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/lumpy.nix b/pkgs/lumpy.nix
index 74dece0..de4d0a3 100644
--- a/pkgs/lumpy.nix
+++ b/pkgs/lumpy.nix
@@ -20,14 +20,14 @@ stdenv.mkDerivation rec {
     cp -r bin "$out"
     substituteInPlace "$out/bin/lumpyexpress.config" \
       --replace "$PWD/" "$out"
-    mkdir -p "$out/lib/lumpy"
+    mkdir -p "$out/lib/lumpy/bamkit"
     for script in \
       pairend_distro.py \
       bamkit/bamgroupreads.py \
       bamkit/bamfilterrg.py \
       bamkit/bamlibs.py
     do
-      cp "scripts/$script" "$out/lib/lumpy"
+      cp "scripts/$script" "$out/lib/lumpy/$script"
       substituteInPlace "$out/bin/lumpyexpress.config" \
         --replace "$out/scripts/$script" "$out/lib/lumpy/$script"
     done