From f0c0e2acc6082503dcb866206cac6843da8d4da8 Mon Sep 17 00:00:00 2001 From: Orivej Desh 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 48548bd7265..2ee9144b316 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 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 87e708526ef..c4b4bb522c4 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 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 2947515652e..323ca90f0a2 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-${version}"; - version = "2017-03-07"; + version = "2018-07-22"; src = fetchFromGitHub { owner = "andyrimmer"; repo = "Platypus"; - rev = "cbbd914"; - sha256 = "0xgj3pl7n4c12j5pp5qyjfk4rsvb5inwzrpcbhdf3br5f3mmdsb9"; + rev = "3e72641c69800da0cd4906b090298e654d316ee1"; + sha256 = "0nah6r54b8xm778gqyb8b7rsd76z8ji4g73sm6rvpw5s96iib1vw"; }; buildInputs = [ htslib python zlib makeWrapper ]; From e78cf6ecbacd4035243d1d75de4a62e407dcf324 Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Fri, 21 Sep 2018 22:48:56 +0000 Subject: [PATCH 4/4] python.pkgs.pysam: 0.13.0 -> 0.15.1 --- pkgs/development/python-modules/pysam/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix index 9d6cbacc958..3138c114e69 100644 --- a/pkgs/development/python-modules/pysam/default.nix +++ b/pkgs/development/python-modules/pysam/default.nix @@ -14,7 +14,7 @@ buildPythonPackage rec { pname = "pysam"; - version = "0.13.0"; + version = "0.15.1"; # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is # missing some files which cause test failures. @@ -23,7 +23,7 @@ buildPythonPackage rec { owner = "pysam-developers"; repo = "pysam"; rev = "v${version}"; - sha256 = "1lwbcl38w1x0gciw5psjp87msmv9zzkgiqikg9b83dqaw2y5az1i"; + sha256 = "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"; }; buildInputs = [ bzip2 curl cython lzma zlib ];