From c3babc9eb65dc8c56d07ce8a6ee0d8c03bbd223e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 9 Jan 2019 16:38:42 +1100
Subject: large refactor

- use bionix.pkgs instead of nixpkgs
- replace stdenv.mkDerivation with stage
---
 tools/gridss-assemble.nix | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'tools/gridss-assemble.nix')

diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index f57bc12..e5cb3ca 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , indexAttrs ? {}
@@ -9,9 +8,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -36,9 +35,9 @@ in
 assert (all sorted inputs);
 assert (homoRef);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-assemble";
-  buildInputs = [ jre bwa ];
+  buildInputs = with pkgs; [ jre bwa ];
   buildCommand = ''
     TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
-- 
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