From 1f99fd69658c6be008296fa61b1a835d1e34d63c Mon Sep 17 00:00:00 2001
From: Orivej Desh <orivej@gmx.fr>
Date: Fri, 1 Dec 2017 00:36:15 +0000
Subject: [PATCH] libminc: fix build after hdf5 upgrade by using hdf5_1_8

---
 .../science/biology/minc-tools/default.nix       | 16 ++++++++++------
 pkgs/development/libraries/libminc/default.nix   | 16 ++++++++++------
 pkgs/top-level/aliases.nix                       |  1 +
 pkgs/top-level/all-packages.nix                  |  6 ++++--
 4 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix
index aae0cf40cee3..7864658c9582 100644
--- a/pkgs/applications/science/biology/minc-tools/default.nix
+++ b/pkgs/applications/science/biology/minc-tools/default.nix
@@ -1,12 +1,14 @@
-{ stdenv, fetchurl, perl, cmake, flex, bison, libminc }:
+{ stdenv, fetchFromGitHub, perl, cmake, flex, bison, libminc }:
 
 stdenv.mkDerivation rec {
-  _name = "minc-tools";
-  name  = "${_name}-2.3.00";
+  name = "${pname}-2.3.00";
+  pname = "minc-tools";
 
-  src = fetchurl {
-    url = "https://github.com/BIC-MNI/${_name}/archive/${_name}-2-3-00.tar.gz";
-    sha256 = "1d457vrwy2fl6ga2axnwn1cchkx2rmgixfzyb1zjxb06cxkfj1dm";
+  src = fetchFromGitHub {
+    owner = "BIC-MNI";
+    repo = pname;
+    rev = builtins.replaceStrings [ "." ] [ "-" ] name;
+    sha256 = "0px5paprx4ds9aln3jdg1pywszgyz2aykgkdbj1y8gc1lwcizsl9";
   };
 
   nativeBuildInputs = [ cmake flex bison ] ++ (if doCheck then [ perl ] else [ ]);
@@ -17,6 +19,8 @@ stdenv.mkDerivation rec {
   checkPhase = "ctest";
   doCheck = false;
 
+  enableParallelBuilding = true;
+
   meta = with stdenv.lib; {
     homepage = https://github.com/BIC-MNI/minc-tools;
     description = "Command-line utilities for working with MINC files";
diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix
index 217ce20c6cfb..673b572c0899 100644
--- a/pkgs/development/libraries/libminc/default.nix
+++ b/pkgs/development/libraries/libminc/default.nix
@@ -1,12 +1,14 @@
-{ stdenv, fetchurl, cmake, zlib, netcdf, hdf5 }:
+{ stdenv, fetchFromGitHub, cmake, zlib, netcdf, hdf5 }:
 
 stdenv.mkDerivation rec {
-  _name = "libminc";
-  name  = "${_name}-2.3.00";
+  name = "${pname}-2.3.00";
+  pname = "libminc";
 
-  src = fetchurl {
-    url = "https://github.com/BIC-MNI/${_name}/archive/${_name}-2-3-00.tar.gz";
-    sha256 = "04ngqx4wkssxs9qqcgq2bvfs1cldcycmpcx587wy3b3m6lwf004c";
+  src = fetchFromGitHub {
+    owner = "BIC-MNI";
+    repo = pname;
+    rev = builtins.replaceStrings [ "." ] [ "-" ] name;
+    sha256 = "1gv1rq1q1brhglll2256cm6sns77ph6fvgbzk3ihkzq46y07yi9s";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -18,6 +20,8 @@ stdenv.mkDerivation rec {
   checkPhase = "ctest";
   doCheck = true;
 
+  enableParallelBuilding = true;
+
   meta = with stdenv.lib; {
     homepage = https://github.com/BIC-MNI/libminc;
     description = "Medical imaging library based on HDF5";
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 253248f4cad1..5dcdbc12f6a1 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -105,6 +105,7 @@ mapAliases (rec {
   manpages = man-pages; # added 2015-12-06
   man_db = man-db; # added 2016-05
   midoriWrapper = midori; # added 2015-01
+  minc_tools = minc-tools; # 2017-12
   mlt-qt5 = libsForQt5.mlt;  # added 2015-12-19
   module_init_tools = kmod; # added 2016-04-22
   mssys = ms-sys; # added 2015-12-13
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d1c1cb526370..e7a014c512e7 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -9472,7 +9472,9 @@ with pkgs;
 
   libmilter = callPackage ../development/libraries/libmilter { };
 
-  libminc = callPackage ../development/libraries/libminc { };
+  libminc = callPackage ../development/libraries/libminc {
+    hdf5 = hdf5_1_8;
+  };
 
   libmirage = callPackage ../misc/emulators/cdemu/libmirage.nix { };
 
@@ -18597,7 +18599,7 @@ with pkgs;
 
   mrbayes = callPackage ../applications/science/biology/mrbayes { };
 
-  minc_tools = callPackage ../applications/science/biology/minc-tools { };
+  minc-tools = callPackage ../applications/science/biology/minc-tools { };
 
   ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { };