From 052e4baf0a233f1860a9fe993b9b759c22aa1239 Mon Sep 17 00:00:00 2001
From: Uli Baum <xeji@cat3.de>
Date: Fri, 3 Aug 2018 08:27:41 +0200
Subject: somatic-sniper: disable parallel building

to fix non-deterministic failure
---
 pkgs/applications/science/biology/somatic-sniper/default.nix | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'pkgs/applications/science')

diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix
index adc8648c6980..4bbd6a320035 100644
--- a/pkgs/applications/science/biology/somatic-sniper/default.nix
+++ b/pkgs/applications/science/biology/somatic-sniper/default.nix
@@ -15,6 +15,8 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ cmake zlib ncurses ];
 
+  enableParallelBuilding = false;
+
   meta = with stdenv.lib; {
     description = "Identify single nucleotide positions that are different between tumor and normal";
     license = licenses.mit;
-- 
cgit 1.4.1


From 79cd841713f59a760ac3bcfe0a8960aadea020a6 Mon Sep 17 00:00:00 2001
From: Johannes Frankenau <johannes@frankenau.net>
Date: Fri, 3 Aug 2018 09:08:26 +0200
Subject: bcal: 1.8 -> 1.9

---
 pkgs/applications/science/math/bcal/default.nix | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'pkgs/applications/science')

diff --git a/pkgs/applications/science/math/bcal/default.nix b/pkgs/applications/science/math/bcal/default.nix
index 8db4bd157df6..61eb1fd3ce4e 100644
--- a/pkgs/applications/science/math/bcal/default.nix
+++ b/pkgs/applications/science/math/bcal/default.nix
@@ -1,20 +1,22 @@
-{ stdenv, fetchFromGitHub, python3Packages }:
+{ stdenv, fetchFromGitHub, python3Packages, readline }:
 
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "bcal-${version}";
-  version = "1.8";
+  version = "1.9";
 
   src = fetchFromGitHub {
     owner = "jarun";
     repo = "bcal";
     rev = "v${version}";
-    sha256 = "0jdn46wzwq7yn3x6p1xyqarp52pcr0ghnfhkm7nyxv734g1abw7r";
+    sha256 = "0h6qi5rvzl6c6fsfdpdb3l4jcgip03l18i0b1x08z1y89i56y8mm";
   };
 
   nativeBuildInputs = [ python3Packages.pytest ];
 
+  buildInputs = [ readline ];
+
   doCheck = true;
   checkPhase = ''
     python3 -m pytest test.py
-- 
cgit 1.4.1


From ae3bbf2958ff72cad357074eb24ccc18afab21c3 Mon Sep 17 00:00:00 2001
From: Robert Schütz <robert.schuetz@stud.uni-heidelberg.de>
Date: Fri, 3 Aug 2018 18:04:46 +0200
Subject: almonds: use python3

---
 pkgs/applications/science/math/almonds/default.nix | 8 +++-----
 pkgs/top-level/all-packages.nix                    | 2 +-
 2 files changed, 4 insertions(+), 6 deletions(-)

(limited to 'pkgs/applications/science')

diff --git a/pkgs/applications/science/math/almonds/default.nix b/pkgs/applications/science/math/almonds/default.nix
index fb76699b0c83..96613f4e38a6 100644
--- a/pkgs/applications/science/math/almonds/default.nix
+++ b/pkgs/applications/science/math/almonds/default.nix
@@ -1,11 +1,9 @@
-{ stdenv, buildPythonApplication, fetchFromGitHub, ncurses, pillow, pytest }:
+{ stdenv, python3, fetchFromGitHub, ncurses }:
 
-let
+with python3.pkgs; buildPythonApplication rec {
+  pname = "almonds";
   version = "1.25b";
-in
 
-buildPythonApplication {
-  name = "almonds-${version}";
   src = fetchFromGitHub {
     owner = "Tenchi2xh";
     repo = "Almonds";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 8d151eadf4e3..fdffd26490b0 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -20461,7 +20461,7 @@ with pkgs;
 
   ### SCIENCE/MATH
 
-  almonds = pythonPackages.callPackage ../applications/science/math/almonds { };
+  almonds = callPackage ../applications/science/math/almonds { };
 
   arpack = callPackage ../development/libraries/science/math/arpack { };
 
-- 
cgit 1.4.1