diff options
Diffstat (limited to 'tools/bwa-mem.nix')
| -rw-r--r-- | tools/bwa-mem.nix | 11 |
1 files changed, 5 insertions, 6 deletions
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 2b3bc64..1427b49 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -1,5 +1,4 @@ { bionix -, nixpkgs , ref , bamOutput ? true , flags ? null @@ -10,18 +9,18 @@ , input2 ? null }: -with nixpkgs; +with bionix; with lib; -with bionix.types; -with bionix.compression; +with types; +with compression; let fa = f: matchFiletype "bwa-ref" { fa = _: f; } f; fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f; -in stdenv.mkDerivation { +in stage { name = "bwa-mem"; - buildInputs = [ bwa bc ] ++ optional bamOutput samtools; + buildInputs = with pkgs; [ bwa bc ] ++ optional bamOutput samtools; buildCommand = '' ln -s ${fa ref} ref.fa for f in ${bionix.bwa.index indexAttrs ref}/* ; do |