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.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'tools/gridss.nix')

diff --git a/tools/gridss.nix b/tools/gridss.nix
index 5bb9484..e8dd304 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,14 +1,13 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 rec {
-  jar = fetchurl {
+  jar = pkgs.fetchurl {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
-  gridssConfig = callBionixE ./gridss-configFile.nix {};
+  genConfig = callBionixE ./gridss-configFile.nix {};
   callVariants = callBionixE ./gridss-callVariants.nix;
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
-- 
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