From fbe7543726f4321e3cb11c2fa503c27df14ac8fd Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 20 Jun 2019 08:23:30 +1000
Subject: CNVkit: merge into nixpkgs

---
 tools/cnvkit-app.nix     | 60 ------------------------------------------------
 tools/cnvkit-batch.nix   |  2 +-
 tools/cnvkit-scatter.nix |  2 +-
 tools/cnvkit.nix         |  2 --
 4 files changed, 2 insertions(+), 64 deletions(-)
 delete mode 100644 tools/cnvkit-app.nix

(limited to 'tools')

diff --git a/tools/cnvkit-app.nix b/tools/cnvkit-app.nix
deleted file mode 100644
index dc9f023..0000000
--- a/tools/cnvkit-app.nix
+++ /dev/null
@@ -1,60 +0,0 @@
-{ lib
-, fetchurl
-, rPackages
-, rWrapper
-, buildPythonPackage
-, fetchPypi
-, biopython
-, six
-, numpy
-, pillow
-, pysam
-, future
-, scipy
-, pandas
-, matplotlib
-, reportlab
-, zlib
-, bzip2
-, htslib
-, libjpeg
-, pkgconfig
-, futures
-}:
-
-let pyfaidx = buildPythonPackage rec {
-      pname = "pyfaidx";
-      version = "0.5.3.1";
-
-      src = fetchPypi {
-        inherit pname version;
-        sha256 = "0mjbksbj9hh2cf0yjr951cjahhn0lg7p71kd3kvbnscqyxa44kfr";
-      };
-
-      propagatedBuildInputs = [ six ];
-    };
-
-    cghFLasso = rPackages.buildRPackage rec {
-      name = "cghFLasso-${version}";
-      version = "0.2-1";
-      src = fetchurl {
-        url = "https://cran.r-project.org/src/contrib/Archive/cghFLasso/cghFLasso_${version}.tar.gz";
-        sha256 = "0b1hnjf9g0v47hbz0dy9m6jhcl1ky20yyhhmm8myng2sndcpjsbf";
-      };
-    };
-
-    cnvR = rWrapper.override {
-      packages = with rPackages; [ DNAcopy cghFLasso ];
-    };
-
-in buildPythonPackage rec {
-  pname = "CNVkit";
-  version = "0.9.5";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1sa70bmnxj1lzp33pbj3axk6n77czswwj9cirimxh2qrn84i7vs3";
-  };
-
-  propagatedBuildInputs = [ biopython numpy scipy pandas matplotlib reportlab pyfaidx pysam futures future pillow cnvR ];
-}
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 114b6b9..5160867 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -22,7 +22,7 @@ assert (all sorted (normals ++ tumours));
 
 stage {
   name = "cnvkit";
-  buildInputs = [ cnvkit.app ];
+  buildInputs = with pkgs; [ python3Packages.cnvkit ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
diff --git a/tools/cnvkit-scatter.nix b/tools/cnvkit-scatter.nix
index f9dc7f6..2899584 100644
--- a/tools/cnvkit-scatter.nix
+++ b/tools/cnvkit-scatter.nix
@@ -9,7 +9,7 @@ with types;
 
 stage {
   name = "cnvkit-scatter";
-  buildInputs = [ cnvkit.app ];
+  buildInputs = with pkgs; [ pkgs.python3Packages.cnvkit ];
   buildCommand = ''
     cnvkit.py scatter -s ${input}/*.cn{s,r} -o plot.pdf
     cp plot.pdf $out
diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix
index 73f4329..fc55d94 100644
--- a/tools/cnvkit.nix
+++ b/tools/cnvkit.nix
@@ -3,8 +3,6 @@
 with bionix;
 
 {
-  app = lib.callPackageWith (pkgs // pkgs.pythonPackages) ./cnvkit-app.nix {};
-
   /* Call CNVs
   Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
   */
-- 
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