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| author | Justin Bedo <cu@cua0.org> | 2018-09-26 14:58:34 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-09-26 14:58:34 +1000 |
| commit | 9de0e998ef5fe8f53412a77f99862bc9f5c15f24 (patch) | |
| tree | 18e6e3f43bc6d7d5d3a5b8a7375c903d4c70eb19 /tools/bwa-mem.nix | |
| parent | b4da5a5b3564e644975c90dad0ef32073b6513a9 (diff) | |
move bwa index to parameters
Diffstat (limited to 'tools/bwa-mem.nix')
| -rw-r--r-- | tools/bwa-mem.nix | 7 |
1 files changed, 3 insertions, 4 deletions
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 5a2772e..9af3992 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -3,6 +3,7 @@ , lib , bc , bwa +, index ? callPackage ./bwa-index.nix { inherit bwa stdenv lib; } , samtools ? null , ref , bamOutput ? true @@ -17,14 +18,12 @@ assert bamOutput -> samtools != null; with lib; -let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref; - -in stdenv.mkDerivation { +stdenv.mkDerivation { name = "bwa-mem"; buildInputs = [ bwa bc ] ++ optional bamOutput samtools; buildCommand = '' ln -s ${ref} ref.fa - for f in ${index}/* ; do + for f in ${index ref}/* ; do ln -s $f done cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) |