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-callVariants.nix | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

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

diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index d55db23..4117126 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
@@ -8,9 +7,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -22,9 +21,9 @@ in
 
 assert (length (unique refs) == 1);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-callVariants";
-  buildInputs = [ jre R bwa ];
+  buildInputs = with pkgs; [ jre R bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
-- 
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