Merge pull request #38664 from bcdarwin/minc_ecosystem

MINC ecosystem

9 files changed, 220 insertions, 13 deletions

diff --git a/pkgs/applications/graphics/c3d/default.nix b/pkgs/applications/graphics/c3d/default.nix
index 74631e88ebfb..7e1c6d7c8c4b 100644
--- a/pkgs/applications/graphics/c3d/default.nix
+++ b/pkgs/applications/graphics/c3d/default.nix
@@ -3,12 +3,12 @@
 stdenv.mkDerivation rec {
   name    = "${pname}-${version}";
   pname   = "c3d";
-  version = "1.1.0";
+  version = "2018-10-04";
 
   src = fetchgit {
     url = "https://git.code.sf.net/p/c3d/git";
-    rev = "3453f6133f0df831dcbb0d0cfbd8b26e121eb153";
-    sha256 = "1xgbk20w22jwvf7pa0n4lcbyx35fq56zzlslj0nvcclh6vx0b4z8";
+    rev = "351929a582b2ef68fb9902df0b11d38f44a0ccd0";
+    sha256 = "0mpv4yl6hdnxgvnwrmd182h64n3ppp30ldzm0jz6jglk0nvpzq9w";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -21,5 +21,6 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
     license = licenses.gpl2;
+    broken = true;
   };
 }
diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix
new file mode 100644
index 000000000000..20d88eb3aafb
--- /dev/null
+++ b/pkgs/applications/science/biology/EZminc/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, itk, fftwFloat, gsl }:
+
+stdenv.mkDerivation rec { pname = "EZminc";
+  name  = "${pname}-2017-08-29";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "4e017236cb6e7f6e07507446b18b759c584b6fc3";
+    sha256 = "1pg06x42pgsg7zy7dz9wf6ajakkm2n8by64lg9z64qi8qqy82b8v";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ itk libminc bicpl fftwFloat gsl ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
+                 "-DEZMINC_BUILD_TOOLS=TRUE"
+                 "-DEZMINC_BUILD_MRFSEG=TRUE"
+                 "-DEZMINC_BUILD_DD=TRUE" ];
+
+  checkPhase = "ctest --output-on-failure ../tests/";  # but ctest doesn't find the tests ...
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BIC-MNI/${pname}";
+    description = "Collection of Perl and shell scripts for processing MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license = licenses.free;
+  };
+}
diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix
new file mode 100644
index 000000000000..c14846beec2f
--- /dev/null
+++ b/pkgs/applications/science/biology/N3/default.nix
@@ -0,0 +1,38 @@
+{ stdenv, fetchFromGitHub, cmake, makeWrapper,
+  perl, MNI-Perllib, GetoptTabular,
+  libminc, EBTKS }:
+
+stdenv.mkDerivation rec {
+  pname = "N3";
+  name  = "${pname}-2017-09-18";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d";
+    sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g";
+  };
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc EBTKS ];
+  propagatedBuildInputs = [ perl MNI-Perllib GetoptTabular ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+
+  checkPhase = "ctest --output-on-failure";
+  # don't run the tests as they fail at least due to missing program wrappers in this phase ...
+
+  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 = "MRI non-uniformity correction for MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}
diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix
new file mode 100644
index 000000000000..f17143ad06bb
--- /dev/null
+++ b/pkgs/applications/science/biology/inormalize/default.nix
@@ -0,0 +1,39 @@
+{ stdenv, fetchFromGitHub, cmake, makeWrapper,
+  perl, GetoptTabular, MNI-Perllib,
+  libminc, EBTKS }:
+
+stdenv.mkDerivation rec {
+  pname = "inormalize";
+  name  = "${pname}-2014-10-21";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f";
+    sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7";
+  };
+
+  patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ];
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc EBTKS ];
+  propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${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;
+    license   = licenses.free;
+  };
+}
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/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix
index 7864658c9582..8e1f74686d1f 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}-2017-09-11";
 
   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;
 
@@ -26,5 +32,6 @@ stdenv.mkDerivation rec {
     description = "Command-line utilities for working with MINC files";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
+    license   = licenses.free;
   };
 }
diff --git a/pkgs/applications/science/biology/minc-widgets/default.nix b/pkgs/applications/science/biology/minc-widgets/default.nix
new file mode 100644
index 000000000000..9084dfb2e1c3
--- /dev/null
+++ b/pkgs/applications/science/biology/minc-widgets/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, cmake, makeWrapper,
+  perl, GetoptTabular, MNI-Perllib,
+  libminc, octave, coreutils, minc_tools }:
+
+stdenv.mkDerivation rec {
+  pname = "minc-widgets";
+  name  = "${pname}-2016-04-20";
+
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "f08b643894c81a1a2e0fbfe595a17a42ba8906db";
+    sha256 = "1b9g6lf37wpp211ikaji4rf74rl9xcmrlyqcw1zq3z12ji9y33bm";
+  };
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc ];
+  propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib octave coreutils minc_tools ];
+
+  postFixup = ''
+    for p in $out/bin/*; do
+      wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}";
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BIC-MNI/${pname}";
+    description = "Collection of Perl and shell scripts for processing MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license = licenses.free;
+  };
+}
diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix
new file mode 100644
index 000000000000..076ecd03a1b1
--- /dev/null
+++ b/pkgs/applications/science/biology/mni_autoreg/default.nix
@@ -0,0 +1,36 @@
+{ stdenv, fetchFromGitHub, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }:
+
+stdenv.mkDerivation rec {
+  pname = "mni_autoreg";
+  name  = "${pname}-2017-09-22";
+
+  src = fetchFromGitHub {
+    owner = "BIC-MNI";
+    repo = pname;
+    rev = "ab99e29987dc029737785baebf24896ec37a2d76";
+    sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq";
+  };
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc ];
+  propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ];
+  # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc
+
+  postFixup = ''
+    for prog in autocrop mritoself mritotal xfmtool; do
+      echo $out/bin/$prog
+      wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB;
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/BIC-MNI/mni_autoreg;
+    description = "Tools for automated registration using the MINC image format";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license = licenses.free;
+  };
+}
+