large refactor

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

1 files changed, 4 insertions, 5 deletions

diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
index b791534..e1ca0a8 100644
--- a/tools/samtools-view.nix
+++ b/tools/samtools-view.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , nameSort ? false
 , flags ? null
 , outfmt ? null
@@ -7,9 +6,9 @@
 
 input:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: true; } input);
 
@@ -17,9 +16,9 @@ let
   outfmtR = if outfmt != null then outfmt input else input.filetype;
   fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
   outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
-in stdenv.mkDerivation {
+in stage {
   name = "samtools-view";
-  buildInputs = [ samtools ];
+  buildInputs = with pkgs; [ samtools ];
   buildCommand = ''
     samtools view ${outfmtFlags} ${optionalString (flags != null) flags} ${input} > $out
   '';