diff options
Diffstat (limited to 'tools/samtools-sort.nix')
| -rw-r--r-- | tools/samtools-sort.nix | 7 |
1 files changed, 3 insertions, 4 deletions
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix index 37df5c8..6f9eb33 100644 --- a/tools/samtools-sort.nix +++ b/tools/samtools-sort.nix @@ -1,5 +1,4 @@ { bionix -, nixpkgs , nameSort ? false , flags ? null , outfmt ? null @@ -7,7 +6,7 @@ input: -with nixpkgs; +with bionix; with lib; let @@ -20,9 +19,9 @@ let outfmtR = if outfmt != null then outfmt input else input.filetype; outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;}; alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; none = _: false;} input; -in stdenv.mkDerivation { +in pkgs.stdenv.mkDerivation { name = "samtools-sort"; - buildInputs = [ samtools ]; + buildInputs = with pkgs; [ samtools ]; buildCommand = if alreadySorted then "ln -s ${input} $out" |