From f0c0e2acc6082503dcb866206cac6843da8d4da8 Mon Sep 17 00:00:00 2001
From: Orivej Desh <orivej@gmx.fr>
Date: Fri, 21 Sep 2018 22:41:06 +0000
Subject: [PATCH 1/4] htslib: 1.7 -> 1.9

---
 pkgs/development/libraries/science/biology/htslib/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix
index 48548bd72652..2ee9144b316d 100644
--- a/pkgs/development/libraries/science/biology/htslib/default.nix
+++ b/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "htslib";
-  version = "1.7";
+  version = "1.9";
 
   src = fetchurl {
     url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "be3d4e25c256acdd41bebb8a7ad55e89bb18e2fc7fc336124b1e2c82ae8886c6";
+    sha256 = "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0";
   };
 
   # perl is only used during the check phase.

From cefd38b721e7dda1a841a12cd2eaec4825276202 Mon Sep 17 00:00:00 2001
From: Orivej Desh <orivej@gmx.fr>
Date: Fri, 21 Sep 2018 22:41:24 +0000
Subject: [PATCH 2/4] samtools: 1.8 -> 1.9

---
 pkgs/applications/science/biology/samtools/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index 87e708526ef7..c4b4bb522c40 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "samtools";
-  version = "1.8";
+  version = "1.9";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9";
+    sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8";
   };
 
   nativeBuildInputs = [ perl ];

From 7545b7dcf3d5857d40bf3e9171074d46514d0f0e Mon Sep 17 00:00:00 2001
From: Orivej Desh <orivej@gmx.fr>
Date: Fri, 21 Sep 2018 22:41:51 +0000
Subject: [PATCH 3/4] platypus: 2017-03-07 -> 2018-07-22

---
 pkgs/applications/science/biology/platypus/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix
index 2947515652e2..323ca90f0a2a 100644
--- a/pkgs/applications/science/biology/platypus/default.nix
+++ b/pkgs/applications/science/biology/platypus/default.nix
@@ -4,13 +4,13 @@ let python = python27.withPackages (ps: with ps; [ cython ]);
 
 in stdenv.mkDerivation rec {
   name = "platypus-unstable-${version}";
-  version = "2017-03-07";
+  version = "2018-07-22";
 
   src = fetchFromGitHub {
     owner = "andyrimmer";
     repo = "Platypus";
-    rev = "cbbd914";
-    sha256 = "0xgj3pl7n4c12j5pp5qyjfk4rsvb5inwzrpcbhdf3br5f3mmdsb9";
+    rev = "3e72641c69800da0cd4906b090298e654d316ee1";
+    sha256 = "0nah6r54b8xm778gqyb8b7rsd76z8ji4g73sm6rvpw5s96iib1vw";
   };
 
   buildInputs = [ htslib python zlib makeWrapper ];

From e78cf6ecbacd4035243d1d75de4a62e407dcf324 Mon Sep 17 00:00:00 2001
From: Orivej Desh <orivej@gmx.fr>
Date: Fri, 21 Sep 2018 22:48:56 +0000
Subject: [PATCH 4/4] python.pkgs.pysam: 0.13.0 -> 0.15.1

---
 pkgs/development/python-modules/pysam/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index 9d6cbacc9589..3138c114e697 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -14,7 +14,7 @@
 
 buildPythonPackage rec {
   pname   = "pysam";
-  version = "0.13.0";
+  version = "0.15.1";
 
   # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
   # missing some files which cause test failures.
@@ -23,7 +23,7 @@ buildPythonPackage rec {
     owner = "pysam-developers";
     repo = "pysam";
     rev = "v${version}";
-    sha256 = "1lwbcl38w1x0gciw5psjp87msmv9zzkgiqikg9b83dqaw2y5az1i";
+    sha256 = "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x";
   };
 
   buildInputs = [ bzip2 curl cython lzma zlib ];