From 082b3f1058458713bd56ea096de16f243cb47f32 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Sun, 24 Sep 2017 18:06:00 -0400
Subject: [PATCH] minc-tools: 2.3.00 -> 2.3.01 (develop branch)

---
 .../science/biology/minc-tools/default.nix    | 26 ++++++++++++-------
 pkgs/top-level/all-packages.nix               |  4 ++-
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix
index 7864658c9582..011db3f0fb86 100644
--- a/pkgs/applications/science/biology/minc-tools/default.nix
+++ b/pkgs/applications/science/biology/minc-tools/default.nix
@@ -1,23 +1,29 @@
-{ stdenv, fetchFromGitHub, perl, cmake, flex, bison, libminc }:
+{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, libminc, libjpeg, zlib }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-2.3.00";
   pname = "minc-tools";
+  name  = "${pname}-2.3.01";
 
   src = fetchFromGitHub {
-    owner = "BIC-MNI";
-    repo = pname;
-    rev = builtins.replaceStrings [ "." ] [ "-" ] name;
-    sha256 = "0px5paprx4ds9aln3jdg1pywszgyz2aykgkdbj1y8gc1lwcizsl9";
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "5b7c40425cd4f67a018055cb85c0157ee50a3056";
+    sha256 = "0zkcs05svp1gj5h0cdgc0k20c7lrk8m7wg3ks3xc5mkaiannj8g7";
   };
 
-  nativeBuildInputs = [ cmake flex bison ] ++ (if doCheck then [ perl ] else [ ]);
-  buildInputs = [ libminc ];
+  nativeBuildInputs = [ cmake flex bison makeWrapper ];
+  buildInputs = [ libminc libjpeg zlib ];
+  propagatedBuildInputs = [ perl TextFormat ];
 
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
 
-  checkPhase = "ctest";
-  doCheck = false;
+  checkPhase = "ctest --output-on-failure";  # still some weird test failures though
+
+  postFixup = ''
+    for prog in minccomplete minchistory mincpik; do
+      wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB
+    done
+  '';
 
   enableParallelBuilding = true;
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 03018649317b..6315c140f176 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19759,7 +19759,9 @@ with pkgs;
 
   mrbayes = callPackage ../applications/science/biology/mrbayes { };
 
-  minc-tools = callPackage ../applications/science/biology/minc-tools { };
+  minc_tools = callPackage ../applications/science/biology/minc-tools {
+    inherit (perlPackages) TextFormat;
+  };
 
   ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { };