Merge pull request #38664 from bcdarwin/minc_ecosystem

MINC ecosystem

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;
   };
 }

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;
+  };
+}

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;
+  };
+}

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;
+  };
+}

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 :

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 :

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;
   };
 }

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;
+  };
+}

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;
+  };
+}
+

pkgs/development/libraries/arguments/default.nix

@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, bicpl }:
+
+stdenv.mkDerivation rec {
+  pname = "arguments";
+  name  = "${pname}-2015-11-30";
+
+  owner = "BIC-MNI";
+
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "b3aad97f6b6892cb8733455d0d448649a48fa108";
+    sha256 = "1ar8lm1w1jflz3vdmjr5c4x6y7rscvrj78b8gmrv79y95qrgzv6s";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ ];
+
+  #cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" "-DBUILD_TESTING=FALSE" ];
+
+  checkPhase = "ctest --output-on-failure";
+  doCheck = false;
+  # internal_volume_io.h: No such file or directory
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Library for argument handling for MINC programs";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}

pkgs/development/libraries/itk/default.nix

@@ -12,7 +12,9 @@ stdenv.mkDerivation rec {
     "-DBUILD_TESTING=OFF"
     "-DBUILD_EXAMPLES=OFF"
     "-DBUILD_SHARED_LIBS=ON"
+    "-DModule_ITKMINC=ON"
     "-DModule_ITKIOMINC=ON"
+    "-DModule_ITKIOTransformMINC=ON"
     "-DModule_ITKVtkGlue=ON"
     "-DModule_ITKReview=ON"
   ];

pkgs/development/libraries/libminc/default.nix

@@ -1,31 +1,42 @@
-{ stdenv, fetchFromGitHub, cmake, zlib, netcdf, hdf5 }:
+{ stdenv, fetchFromGitHub, cmake, zlib, netcdf, nifticlib, hdf5 }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-2.3.00";
   pname = "libminc";
+  name  = "${pname}-2017-09-14";
 
+  owner = "BIC-MNI";
+
+  # current master is significantly ahead of most recent release, so use Git version:
   src = fetchFromGitHub {
-    owner = "BIC-MNI";
-    repo = pname;
-    rev = builtins.replaceStrings [ "." ] [ "-" ] name;
-    sha256 = "1gv1rq1q1brhglll2256cm6sns77ph6fvgbzk3ihkzq46y07yi9s";
+    inherit owner;
+    repo   = pname;
+    rev    = "e11c6df9321b4061bf87a7d43171ec55e9e3908f";
+    sha256 = "0lmd0js3jgni2mw1zfvd4qg6byxiv3ndgv2z3nm7975i83zw48xk";
   };
 
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ zlib netcdf hdf5 ];
+  buildInputs = [ zlib netcdf nifticlib hdf5 ];
 
-  cmakeFlags = [ "-DBUILD_TESTING=${if doCheck then "ON" else "OFF"}"
-                 "-DLIBMINC_MINC1_SUPPORT=ON" ];
+  cmakeFlags = [ "-DBUILD_TESTING=${if doCheck then "TRUE" else "FALSE"}"
+                 "-DLIBMINC_MINC1_SUPPORT=TRUE"
+                 "-DLIBMINC_BUILD_SHARED_LIBS=TRUE"
+                 "-DLIBMINC_USE_SYSTEM_NIFTI=TRUE" ];
 
-  checkPhase = "ctest";
+
+  checkPhase = ''
+    export LD_LIBRARY_PATH="$(pwd)"  # see #22060
+    ctest -E 'ezminc_rw_test|minc_conversion' --output-on-failure
+    # ezminc_rw_test can't find libminc_io.so.5.2.0; minc_conversion hits netcdf compilation issue
+  '';
   doCheck = true;
 
   enableParallelBuilding = true;
 
   meta = with stdenv.lib; {
-    homepage = https://github.com/BIC-MNI/libminc;
+    homepage = "https://github.com/${owner}/${pname}";
     description = "Medical imaging library based on HDF5";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
+    license   = licenses.free;
   };
 }

pkgs/development/libraries/science/biology/EBTKS/default.nix

@@ -0,0 +1,28 @@
+{ stdenv, fetchFromGitHub, cmake, libminc }:
+
+stdenv.mkDerivation rec {
+  pname = "EBTKS";
+  name  = "${pname}-2017-09-23";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";
+    sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+
+  checkPhase = "ctest --output-on-failure";  # but cmake doesn't run the tests ...
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BIC-MNI/${pname}";
+    description = "Library for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}

pkgs/development/libraries/science/biology/bicpl/default.nix

@@ -0,0 +1,33 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, netpbm }:
+
+stdenv.mkDerivation rec {
+  pname = "bicpl";
+  name  = "${pname}-2017-09-10";
+
+  owner = "BIC-MNI";
+
+  # current master is significantly ahead of most recent release, so use Git version:
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "612a63e740fadb162fcf27ee00da6a18dec4d5a9";
+    sha256 = "1vv9gi184bkvp3f99v9xmmw1ly63ip5b09y7zdjn39g7kmwzrga7";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc netpbm ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBUILD_TESTING=FALSE" ];
+
+  checkPhase = "ctest --output-on-failure";
+  doCheck = false;
+  # internal_volume_io.h: No such file or directory
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Brain Imaging Centre programming library";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}

pkgs/development/libraries/science/biology/elastix/default.nix

@@ -1,22 +1,18 @@
-{ stdenv, fetchFromGitHub, cmake, itk, python }:
+{ stdenv, fetchurl, cmake, itk, python }:
 
 stdenv.mkDerivation rec {
-  _name    = "elastix";
-  _version = "4.8";
-  name  = "${_name}-${_version}";
+  pname    = "elastix";
+  pversion = "4.9.0";
+  name  = "${pname}-${pversion}";
 
-  src = fetchFromGitHub {
-    owner  = "SuperElastix";
-    repo   = "elastix";
-    rev    = "ef057ff89233822b26b04b31c3c043af57d5deff";
-    sha256 = "0gm3a8dgqww50h6zld9ighjk92wlpybpimjwfz4s5h82vdjsvxrm";
+  src = fetchurl {
+    url    = "https://github.com/SuperElastix/${pname}/archive/${pversion}.tar.gz";
+    sha256 = "02pbln36nq98xxfyqwlxg7b6gmigdq4fgfqr9mym1qn58aj04shg";
   };
 
   nativeBuildInputs = [ cmake python ];
   buildInputs = [ itk ];
 
-  cmakeFlags = [ "-DUSE_KNNGraphAlphaMutualInformationMetric=OFF" ];
-
   checkPhase = "ctest";
 
   meta = with stdenv.lib; {

pkgs/development/libraries/science/biology/oobicpl/default.nix

@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }:
+
+stdenv.mkDerivation rec {
+  pname = "oobicpl";
+  name  = "${pname}-2016-03-02";
+
+  owner = "BIC-MNI";
+
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "bc062a65dead2e58461f5afb37abedfa6173f10c";
+    sha256 = "05l4ml9djw17bgdnrldhcxydrzkr2f2scqlyak52ph5azj5n4zsx";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc bicpl arguments pcre-cpp ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib"
+                 "-DBICPL_DIR=${bicpl}/lib"
+                 "-DARGUMENTS_DIR=${arguments}/lib"
+                 "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Brain Imaging Centre object-oriented programming library (and tools)";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}

pkgs/development/perl-modules/MNI/default.nix

@@ -0,0 +1,21 @@
+{ fetchFromGitHub, buildPerlPackage, stdenv, perl }:
+
+buildPerlPackage rec {
+  name = "MNI-Perllib-2012-04-13";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = "mni-perllib";
+    rev    = "b908472b4390180ea5d19a121ac5edad6ed88d83";
+    sha256 = "0vk99pwgbard62k63386r7dpnm3h435jdqywr4xqfq7p04dz6kyb";
+  };
+
+  patches = [ ./no-stdin.patch ];
+
+  doCheck = false;  # TODO: almost all tests fail ... is this a real problem?
+
+  meta = with stdenv.lib; {
+    license = with licenses; [ artistic1 gpl1Plus ];
+    maintainers = with maintainers; [ bcdarwin ];
+  };
+}

pkgs/development/perl-modules/MNI/no-stdin.patch

@@ -0,0 +1,13 @@
+diff --git a/Makefile.PL b/Makefile.PL
+index 9f2039a..12d699c 100644
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -213,7 +213,7 @@ TEXT
+ }  # &MY::postamble
+ 
+ 
+-query_subs;
++#query_subs;
+ 
+ my $f;
+ WriteMakefile 

pkgs/top-level/aliases.nix

@@ -130,7 +130,6 @@ mapAliases (rec {
   man_db = man-db; # added 2016-05
   piwik = matomo; # added 2018-01-16
   midoriWrapper = midori; # added 2015-01
-  minc_tools = minc-tools; # 2017-12
   mlt-qt5 = libsForQt5.mlt;  # added 2015-12-19
   mobile_broadband_provider_info = mobile-broadband-provider-info; # added 2018-02-25
   module_init_tools = kmod; # added 2016-04-22

pkgs/top-level/all-packages.nix

@@ -519,6 +519,8 @@ with pkgs;
 
   apitrace = libsForQt5.callPackage ../applications/graphics/apitrace {};
 
+  arguments = callPackage ../development/libraries/arguments { };
+
   argus = callPackage ../tools/networking/argus {};
 
   argus-clients = callPackage ../tools/networking/argus-clients {};
@@ -1142,6 +1144,8 @@ with pkgs;
 
   earlyoom = callPackage ../os-specific/linux/earlyoom { };
 
+  EBTKS = callPackage ../development/libraries/science/biology/EBTKS { };
+
   ecasound = callPackage ../applications/audio/ecasound { };
 
   edac-utils = callPackage ../os-specific/linux/edac-utils { };
@@ -8477,6 +8481,8 @@ with pkgs;
 
   libopcodes = callPackage ../development/libraries/libopcodes { };
 
+  bicpl = callPackage ../development/libraries/science/biology/bicpl { };
+
   # TODO(@Ericson2314): Build bionic libc from source
   bionic = assert hostPlatform.useAndroidPrebuilt;
     androidenv.androidndkPkgs.libraries;
@@ -10772,6 +10778,8 @@ with pkgs;
 
   oniguruma = callPackage ../development/libraries/oniguruma { };
 
+  oobicpl = callPackage ../development/libraries/science/biology/oobicpl { };
+
   openal = self.openalSoft;
 
   openalSoft = callPackage ../development/libraries/openal-soft {
@@ -19741,10 +19749,16 @@ with pkgs;
 
   emboss = callPackage ../applications/science/biology/emboss { };
 
+  ezminc = callPackage ../applications/science/biology/EZminc { };
+
   htslib = callPackage ../development/libraries/science/biology/htslib { };
 
   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;
   };
@@ -19753,6 +19767,10 @@ with pkgs;
 
   muscle = callPackage ../applications/science/biology/muscle/default.nix { };
 
+  n3 = callPackage ../applications/science/biology/N3 {
+    inherit (perlPackages) perl GetoptTabular MNI-Perllib;
+  };
+
   neuron = callPackage ../applications/science/biology/neuron {
     python = null;
   };
@@ -19765,7 +19783,17 @@ 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;
+  };
+
+  minc_widgets = callPackage ../applications/science/biology/minc-widgets {
+    inherit (perlPackages) GetoptTabular MNI-Perllib;
+  };
+
+  mni_autoreg = callPackage ../applications/science/biology/mni_autoreg {
+    inherit (perlPackages) GetoptTabular MNI-Perllib;
+  };
 
   ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { };
 

pkgs/top-level/perl-packages.nix

@@ -9634,6 +9634,8 @@ let self = _self // overrides; _self = with self; {
     };
   };
 
+  MNI-Perllib = pkgs.callPackage ../development/perl-modules/MNI {};
+
   Mo = buildPerlPackage rec {
      name = "Mo-0.40";
      src = fetchurl {
@@ -9661,6 +9663,7 @@ let self = _self // overrides; _self = with self; {
 
   ModernPerl = buildPerlModule {
     name = "Modern-Perl-1.20170117";
+
     src = fetchurl {
       url = mirror://cpan/authors/id/C/CH/CHROMATIC/Modern-Perl-1.20170117.tar.gz;
       sha256 = "5df2a83461163212db22b9c3353606a1a123616820fe50675041c34f004b3628";
@@ -16236,6 +16239,21 @@ let self = _self // overrides; _self = with self; {
     };
   };
 
+  TextFormat = buildPerlPackage rec {
+    name = "Text-Format-0.60";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/S/SH/SHLOMIF/${name}.tar.gz";
+      sha256 = "664f313570604624ff9e1fc9b26b6d04e06897b3e4eac83089fc0905a692a2b8";
+    };
+    buildInputs = [ ModuleBuild ];
+    meta = {
+      homepage = http://www.shlomifish.org/open-source/projects/Text-Format/;
+      description = "Format text";
+      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
+      maintainers = with maintainers; [ bcdarwin ];
+    };
+  };
+
   TextGerman = buildPerlPackage rec {
      name = "Text-German-0.06";
      src = fetchurl {