diff options
Diffstat (limited to 'tools/gridss-assemble.nix')
| -rw-r--r-- | tools/gridss-assemble.nix | 9 |
1 files changed, 4 insertions, 5 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index f57bc12..e5cb3ca 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -1,5 +1,4 @@ { bionix -, nixpkgs , bwaIndexAttrs ? {} , faidxAttrs ? {} , indexAttrs ? {} @@ -9,9 +8,9 @@ , heapSize ? "31g" }: -with nixpkgs; +with bionix; with lib; -with bionix.types; +with types; inputs: @@ -36,9 +35,9 @@ in assert (all sorted inputs); assert (homoRef); -stdenv.mkDerivation rec { +stage rec { name = "gridss-assemble"; - buildInputs = [ jre bwa ]; + buildInputs = with pkgs; [ jre bwa ]; buildCommand = '' TMPDIR=$(pwd) ln -s ${ref} ref.fa |