From e90d1e8631d62053b9f16343baececda9e92406f Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Mon, 25 Sep 2017 14:20:56 -0400
Subject: inormalize: init at 1.0.20 (develop branch)

---
 .../science/biology/inormalize/default.nix         | 38 ++++++++++++++++++++++
 .../science/biology/inormalize/lgmask-interp.patch | 10 ++++++
 .../inormalize/nu_correct_norm-interp.patch        | 10 ++++++
 pkgs/top-level/all-packages.nix                    |  4 +++
 4 files changed, 62 insertions(+)
 create mode 100644 pkgs/applications/science/biology/inormalize/default.nix
 create mode 100644 pkgs/applications/science/biology/inormalize/lgmask-interp.patch
 create mode 100644 pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch

diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix
new file mode 100644
index 000000000000..d202db8521cf
--- /dev/null
+++ b/pkgs/applications/science/biology/inormalize/default.nix
@@ -0,0 +1,38 @@
+{ stdenv, fetchFromGitHub, cmake, makeWrapper,
+  perl, GetoptTabular, MNI-Perllib,
+  libminc, EBTKS }:
+
+stdenv.mkDerivation rec {
+  pname = "inormalize";
+  name  = "${pname}-1.0.20";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f";
+    sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7";
+  };
+
+  patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ];
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc EBTKS ];
+  propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+
+  checkPhase = "ctest --output-on-failure";  # but no tests
+
+  postFixup = ''
+    for p in $out/bin/*; do
+      wrapProgram $p --prefix PERL5LIB : $PERL5LIB
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BIC-MNI/${pname}";
+    description = "Program to normalize intensity of MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/applications/science/biology/inormalize/lgmask-interp.patch b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch
new file mode 100644
index 000000000000..953bce9a1848
--- /dev/null
+++ b/pkgs/applications/science/biology/inormalize/lgmask-interp.patch
@@ -0,0 +1,10 @@
+diff --git a/lgmask.in b/lgmask.in
+index 17dbe4d..2195d91 100644
+--- a/lgmask.in
++++ b/lgmask.in
+@@ -1,4 +1,4 @@
+-#! @PERL@
++#! /usr/bin/env perl
+ 
+ #---------------------------------------------------------------------------
+ #@COPYRIGHT :
diff --git a/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch
new file mode 100644
index 000000000000..75dc46a799ce
--- /dev/null
+++ b/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch
@@ -0,0 +1,10 @@
+diff --git a/nu_correct_norm.in b/nu_correct_norm.in
+index 1dc84ac..1bc6235 100644
+--- a/nu_correct_norm.in
++++ b/nu_correct_norm.in
+@@ -1,4 +1,4 @@
+-#! @PERL@
++#! /usr/bin/perl
+  
+ #---------------------------------------------------------------------------
+ #@COPYRIGHT :
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 51edd6d16e03..cd34788fc39b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19741,6 +19741,10 @@ with pkgs;
 
   igv = callPackage ../applications/science/biology/igv { };
 
+  inormalize = callPackage ../applications/science/biology/inormalize {
+    inherit (perlPackages) GetoptTabular MNI-Perllib;
+  };
+
   iv = callPackage ../applications/science/biology/iv {
     neuron-version = neuron.version;
   };
-- 
cgit 1.4.1