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| author | Justin Bedo <cu@cua0.org> | 2020-07-08 10:55:48 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-07-08 10:56:10 +1000 |
| commit | 0035049b0d2fcd973d544c505a92a3796ab5c22e (patch) | |
| tree | 79c04bc56b4a868dd9a49139f45935cdb9263df5 | |
| parent | 21a643bc66c27a5fba8b9a0683a34160ca05acf2 (diff) | |
cnvkit: python 2 -> python 3
| -rw-r--r-- | tools/cnvkit-batch.nix | 2 | ||||
| -rw-r--r-- | tools/cnvkit-scatter.nix | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix index d6d439d..113e0c9 100644 --- a/tools/cnvkit-batch.nix +++ b/tools/cnvkit-batch.nix @@ -22,7 +22,7 @@ assert (all sorted (normals ++ tumours)); stage { name = "cnvkit"; - buildInputs = with pkgs; [ python2Packages.cnvkit ]; + buildInputs = with pkgs; [ python3Packages.cnvkit ]; outputs = [ "out" ] ++ builtins.genList (x: "out${toString (x + 1)}") (length tumours); buildCommand = '' ln -s ${ref} ref.fa diff --git a/tools/cnvkit-scatter.nix b/tools/cnvkit-scatter.nix index fb7329f..2899584 100644 --- a/tools/cnvkit-scatter.nix +++ b/tools/cnvkit-scatter.nix @@ -9,7 +9,7 @@ with types; stage { name = "cnvkit-scatter"; - buildInputs = with pkgs; [ pkgs.python2Packages.cnvkit ]; + buildInputs = with pkgs; [ pkgs.python3Packages.cnvkit ]; buildCommand = '' cnvkit.py scatter -s ${input}/*.cn{s,r} -o plot.pdf cp plot.pdf $out |