From ee2c76693e0ac2917fc74c737e0eee18a852fe6c Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Sat, 30 Sep 2017 19:44:48 +0200
Subject: samtools: 1.5.0 -> 1.6.0

---
 pkgs/applications/science/biology/samtools/default.nix | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

(limited to 'pkgs')

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index f8391a2d6b3c..0f1f4692eb71 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -1,21 +1,31 @@
-{ stdenv, fetchurl, zlib, htslib,  ncurses ? null }:
+{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:
 
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "samtools";
-  major = "1.5";
+  major = "1.6";
   version = "${major}.0";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2";
-    sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5";
+    sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f";
   };
 
   buildInputs = [ zlib ncurses ];
 
+  propagatedBuildInputs = [ htslib ];
+
   configureFlags = [ "--with-htslib=${htslib}" ]
     ++ stdenv.lib.optional (ncurses == null) "--without-curses";
 
+  enableParallelBuilding = true;
+
+  doCheck = true;
+
+  preCheck = ''
+    sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl
+  '';
+
   meta = with stdenv.lib; {
     description = "Tools for manipulating SAM/BAM/CRAM format";
     license = licenses.mit;
-- 
cgit 1.4.1