From bebccf176effdb520f5c1ee0087caf6d10b9cd54 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Sat, 30 Sep 2017 19:45:26 +0200
Subject: [PATCH] bcftools: 1.5.0 -> 1.6.0

---
 .../science/biology/bcftools/default.nix      | 22 +++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index cfd72601d1eb..b6fc8af43249 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,17 +1,22 @@
-{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }:
+{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl, bash }:
 
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "bcftools";
-  major = "1.5";
+  major = "1.6";
   version = "${major}.0";
 
   src = fetchurl {
     url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2";
-    sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz";
+    sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
   };
 
-  buildInputs = [ zlib bzip2 lzma perl ];
+
+  nativeBuildInputs = [ bash ];
+
+  buildInputs = [ zlib bzip2 lzma ];
+
+  propagatedBuildInputs = [ htslib ];
 
   makeFlags = [
     "HSTDIR=${htslib}"
@@ -19,6 +24,15 @@ stdenv.mkDerivation rec {
     "CC=cc"
   ];
 
+  enableParallelBuilding = true;
+
+  doCheck = true;
+
+  preCheck = ''
+    sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl test/csq/{sort-csq,make-csq-test} misc/plot-vcfstats
+    sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl
+  '';
+
   meta = with stdenv.lib; {
     description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";
     license = licenses.mit;