From 295a23a2db2c6aef712864770f92547c1494e307 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Sun, 7 May 2017 22:30:41 +0200
Subject: [PATCH 1/3] htslib: 1.3.2 -> 1.4

---
 .../libraries/science/biology/htslib/default.nix  | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix
index 29fb338c838..a74905b5ba1 100644
--- a/pkgs/development/libraries/science/biology/htslib/default.nix
+++ b/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -1,16 +1,21 @@
-{ stdenv, fetchurl, zlib }:
+{ stdenv, fetchurl, zlib, bzip2, lzma, curl }:
 
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
+  version = "${major}.0";
   pname = "htslib";
-  version = "1.3.2";
+  major = "1.4";
 
   src = fetchurl {
-    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "0iq3blw23s55vkr1z88p9y2dqrb2dybzhl6hz2nlk53ncihrxcdr";
+    url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2";
+    sha256 = "0l1ki3sqfhawfn7fx9v7i2pm725jki4c5zij9j96xka5zwc8iz2w";
   };
 
-  buildInputs = [ zlib ];
+  buildInputs = [ zlib bzip2 lzma curl ];
+
+  configureFlags = "--enable-libcurl"; # optional but strongly recommended
+
+  installFlags = "prefix=$(out)";
 
   meta = with stdenv.lib; {
     description = "A C library for reading/writing high-throughput sequencing data";

From 9073e67568c66038ab8e5649b5944b6419d42b30 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Sun, 7 May 2017 22:31:14 +0200
Subject: [PATCH 2/3] samtools: 1.3.1 -> 1.4

---
 pkgs/applications/science/biology/samtools/default.nix | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index e97af1ea0ee..827c1448693 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -3,14 +3,15 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "samtools";
-  version = "1.3.1";
+  major = "1.4";
+  version = "${major}.0";
 
   src = fetchurl {
-    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc";
+    url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2";
+    sha256 = "1x73c0lxvd58ghrmaqqyp56z7bkmp28a71fk4ap82j976pw5pbls";
   };
 
-  buildInputs = [ zlib ncurses htslib ];
+  buildInputs = [ zlib ncurses ];
 
   configureFlags = [ "--with-htslib=${htslib}" ]
     ++ stdenv.lib.optional (ncurses == null) "--without-curses";

From 8d1bebf83c5f07e30e8c32700d0dfe7fb65008b1 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Sun, 7 May 2017 22:31:35 +0200
Subject: [PATCH 3/3] bcftools: 1.3.1 -> 1.4

---
 .../applications/science/biology/bcftools/default.nix | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index 7ae62b15d34..97e081f908e 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,16 +1,17 @@
-{ stdenv, fetchurl, zlib, htslib }:
+{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }:
 
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "bcftools";
-  version = "1.3.1";
+  major = "1.4";
+  version = "${major}.0";
 
   src = fetchurl {
-    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj";
+    url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2";
+    sha256 = "0k93mq3lf73dch81p4zxi0bdll567acxfa81qzbzkqflgsjb1ccg";
   };
 
-  buildInputs = [ zlib ];
+  buildInputs = [ zlib bzip2 lzma perl ];
 
   makeFlags = [
     "HSTDIR=${htslib}"