From 8110c2ce6ab558de28c051c0a3eaccdcb97a82db Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 6 Sep 2019 10:59:25 +1000
Subject: cnvkit: use python2
---
tools/cnvkit-batch.nix | 2 +-
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 113e0c9..d6d439d 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; [ python3Packages.cnvkit ];
+ buildInputs = with pkgs; [ python2Packages.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 2899584..fb7329f 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.python3Packages.cnvkit ];
+ buildInputs = with pkgs; [ pkgs.python2Packages.cnvkit ];
buildCommand = ''
cnvkit.py scatter -s ${input}/*.cn{s,r} -o plot.pdf
cp plot.pdf $out
--
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