From d3da5cbf449948e5b058cac5b19510c7c0955a55 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 24 Jun 2016 15:08:16 +0200
Subject: [PATCH 1/3] htslib: init at 1.3.1

---
 .../science/biology/htslib/default.nix        | 23 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 25 insertions(+)
 create mode 100644 pkgs/development/libraries/science/biology/htslib/default.nix

diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix
new file mode 100644
index 00000000000..2609861e319
--- /dev/null
+++ b/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "htslib";
+  version = "1.3.1";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6";
+  };
+
+  buildInputs = [ zlib ];
+
+  meta = with stdenv.lib; {
+    description = "A C library for reading/writing high-throughput sequencing data";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}
+
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 65fced534a8..79718fc79e5 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15885,6 +15885,8 @@ in
 
   emboss = callPackage ../applications/science/biology/emboss { };
 
+  htslib = callPackage ../development/libraries/science/biology/htslib { };
+
   neuron = callPackage ../applications/science/biology/neuron { };
 
   neuron-mpi = appendToName "mpi" (neuron.override {

From 14feec44e4a31b4df7ce166e7d7dfef3c7f81e29 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 24 Jun 2016 15:14:08 +0200
Subject: [PATCH 2/3] samtools: refactoring

---
 .../science/biology/samtools/default.nix         | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index 9535609fa78..e97af1ea0ee 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -1,19 +1,25 @@
-{ stdenv, fetchurl, zlib, ncurses }:
+{ stdenv, fetchurl, zlib, htslib,  ncurses ? null }:
 
 stdenv.mkDerivation rec {
-  name = "samtools-${version}";
+  name = "${pname}-${version}";
+  pname = "samtools";
   version = "1.3.1";
 
   src = fetchurl {
-    url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
+    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
     sha256 = "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc";
   };
 
-  buildInputs = [ zlib ncurses ];
+  buildInputs = [ zlib ncurses htslib ];
+
+  configureFlags = [ "--with-htslib=${htslib}" ]
+    ++ stdenv.lib.optional (ncurses == null) "--without-curses";
 
   meta = with stdenv.lib; {
-    description = "Tools (written in C using htslib) for manipulating next-generation sequencing data";
+    description = "Tools for manipulating SAM/BAM/CRAM format";
     license = licenses.mit;
     homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
   };
 }

From d91d245f1607a44532e4237a997e9bf64ebca120 Mon Sep 17 00:00:00 2001
From: mimadrid <mimadrid@ucm.es>
Date: Fri, 24 Jun 2016 15:18:08 +0200
Subject: [PATCH 3/3] bcftools: init at 1.3.1

---
 .../science/biology/bcftools/default.nix      | 26 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/applications/science/biology/bcftools/default.nix

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
new file mode 100644
index 00000000000..d4e4ed5b954
--- /dev/null
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchurl, zlib, htslib }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "bcftools";
+  version = "1.3.1";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj";
+  };
+
+  buildInputs = [ zlib ];
+
+  preBuild = ''
+    makeFlagsArray=("HSTDIR=${htslib}" "prefix=$out")
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 79718fc79e5..11c0641558b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15883,6 +15883,8 @@ in
     stdenv = overrideCC stdenv gcc49;
   };
 
+  bcftools = callPackage ../applications/science/biology/bcftools { };
+
   emboss = callPackage ../applications/science/biology/emboss { };
 
   htslib = callPackage ../development/libraries/science/biology/htslib { };