From 0035049b0d2fcd973d544c505a92a3796ab5c22e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 8 Jul 2020 10:55:48 +1000
Subject: cnvkit: python 2 -> python 3

---
 tools/cnvkit-batch.nix   | 2 +-
 tools/cnvkit-scatter.nix | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'tools')

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
-- 
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