large refactor

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

1 files changed, 0 insertions, 35 deletions

diff --git a/test.nix b/test.nix
deleted file mode 100644
index 9851310..0000000
--- a/test.nix
+++ /dev/null
@@ -1,35 +0,0 @@
-{pkgs ? import <nixpkgs> {}
-,bionix ? import <bionix> {}}:
-
-with pkgs;
-with lib;
-with bionix;
-
-let
-  inherit (types) filetype tagFiletype;
-
-  fetchLocal = path: stdenv.mkDerivation {
-    name = baseNameOf path;
-    buildCommand = "ln -s ${path} $out";
-  };
-  tagfq = path: tagFiletype (filetype.fq {}) (fetchLocal path);
-  tagfa = path: tagFiletype (filetype.fa {}) (fetchLocal path);
-
-  ref = tagfa ./example/ref.fa;
-  alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
-
-  samples = [ {name = "mysample1"; files = {input1 = tagfq ./example/sample1-1.fq; input2 = tagfq ./example/sample1-2.fq;};}
-              {name = "mysample2"; files = {input1 = tagfq ./example/sample2-1.fq; input2 = tagfq ./example/sample2-1.fq;};} ];
-
-  alignments = map (i: samtools.sort {} (alignWithRG i.name i.files)) samples;
-  variants = platypus.call {} alignments;
-
-in stdenv.mkDerivation {
-  name = "myproject";
-  buildCommand = ''
-    mkdir $out
-    ln -s ${variants} $out/platypus.vcf
-    mkdir $out/alignments
-    ${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
-  '';
-}