large refactor

- use bionix.pkgs instead of nixpkgs
- replace stdenv.mkDerivation with stage

1 files changed, 4 insertions, 5 deletions

diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index 5fc4c59..f2fab30 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , dictIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
@@ -9,9 +8,9 @@
 , config ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -20,9 +19,9 @@ let
 in
 
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-extractSVReads";
-  buildInputs = [ jre R ];
+  buildInputs = with pkgs; [ jre R ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai