From 99dc5f4ab0e3ddae4bc27150d8f41a1fdb08eca2 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Sun, 24 Sep 2017 17:28:16 -0400 Subject: [PATCH 01/22] libminc: 2.3.00 -> 2.3.01 (develop branch) --- .../development/libraries/libminc/default.nix | 27 ++++++++++++------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix index 673b572c089..e133e4be01c 100644 --- a/pkgs/development/libraries/libminc/default.nix +++ b/pkgs/development/libraries/libminc/default.nix @@ -1,23 +1,30 @@ -{ 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}-2.3.01"; + # current master significantly ahead of most recent release src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = builtins.replaceStrings [ "." ] [ "-" ] name; - sha256 = "1gv1rq1q1brhglll2256cm6sns77ph6fvgbzk3ihkzq46y07yi9s"; + owner = "BIC-MNI"; + 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="$(pwd)" # see #22060 + ctest -E ezminc_rw_test --output-on-failure # ezminc_rw_test can't find libminc_io.so.5.2.0 + ''; doCheck = true; enableParallelBuilding = true; From fa2cc0e72fc3e978b6132904d2adb2f3005d15d9 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Sun, 24 Sep 2017 17:50:02 -0400 Subject: [PATCH 02/22] perlPackages.TextFormat: init at 0.60 --- pkgs/top-level/perl-packages.nix | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index d455dde6aee..5a7e4000fe5 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -14997,6 +14997,20 @@ let self = _self // overrides; _self = with self; { }; }; + TextFormat = buildPerlPackage rec { + name = "Text-Format-0.60"; + src = fetchurl { + url = "mirror://cpan/authors/id/S/SH/SHLOMIF/${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 ]; + }; + }; + TextGlob = buildPerlPackage rec { name = "Text-Glob-0.09"; src = fetchurl { From 082b3f1058458713bd56ea096de16f243cb47f32 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Sun, 24 Sep 2017 18:06:00 -0400 Subject: [PATCH 03/22] 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 7864658c958..011db3f0fb8 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 : $PERL5LIB + done + ''; enableParallelBuilding = true; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 03018649317..6315c140f17 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19759,7 +19759,9 @@ with pkgs; mrbayes = callPackage ../applications/science/biology/mrbayes { }; - minc-tools = callPackage ../applications/science/biology/minc-tools { }; + minc_tools = callPackage ../applications/science/biology/minc-tools { + inherit (perlPackages) TextFormat; + }; ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { }; From e7d447ce2c86dd1d97d03a274348afce15c9afed Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Sun, 24 Sep 2017 18:11:30 -0400 Subject: [PATCH 04/22] EBTKS: init at 1.6.50 (develop branch) --- .../science/biology/EBTKS/default.nix | 27 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 29 insertions(+) create mode 100644 pkgs/development/libraries/science/biology/EBTKS/default.nix diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix new file mode 100644 index 00000000000..3103eb31fb8 --- /dev/null +++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchFromGitHub, cmake, libminc }: + +stdenv.mkDerivation rec { + pname = "EBTKS"; + name = "${pname}-1.6.50"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c"; + sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ]; + + checkPhase = "ctest --output-on-failure"; # but there are no tests ... + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Library for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6315c140f17..d16043ce274 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -1144,6 +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 { }; From 61864898f3221de40d6ed9fc1a1ec1c64fd01329 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Sun, 24 Sep 2017 18:19:52 -0400 Subject: [PATCH 05/22] perlPackages.MNI-Perllib: init at 0.08 --- pkgs/development/perl-modules/MNI/default.nix | 20 +++++++++++++++++++ .../perl-modules/MNI/no-stdin.patch | 13 ++++++++++++ pkgs/top-level/perl-packages.nix | 4 ++++ 3 files changed, 37 insertions(+) create mode 100644 pkgs/development/perl-modules/MNI/default.nix create mode 100644 pkgs/development/perl-modules/MNI/no-stdin.patch diff --git a/pkgs/development/perl-modules/MNI/default.nix b/pkgs/development/perl-modules/MNI/default.nix new file mode 100644 index 00000000000..806c7703c88 --- /dev/null +++ b/pkgs/development/perl-modules/MNI/default.nix @@ -0,0 +1,20 @@ +{ fetchFromGitHub, buildPerlPackage, stdenv, perl }: + +buildPerlPackage rec { + name = "MNI-Perllib-0.08"; + + 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 = { + license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ]; + }; +} diff --git a/pkgs/development/perl-modules/MNI/no-stdin.patch b/pkgs/development/perl-modules/MNI/no-stdin.patch new file mode 100644 index 00000000000..1e9e791257e --- /dev/null +++ b/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 $f; + WriteMakefile diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index 5a7e4000fe5..c34986db385 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -8983,6 +8983,10 @@ let self = _self // overrides; _self = with self; { }; }; + MNI-Perllib = import ../development/perl-modules/MNI { + inherit buildPerlPackage fetchFromGitHub stdenv perl; + }; + ModernPerl = buildPerlPackage { name = "Modern-Perl-1.20140107"; src = fetchurl { From bd460f54a3de827ce87fcedfa534c6321a4ef7ac Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 25 Sep 2017 11:34:39 -0400 Subject: [PATCH 06/22] mni_autoreg: init at 0.99.70 --- .../science/biology/mni_autoreg/default.nix | 34 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 +++ 2 files changed, 38 insertions(+) create mode 100644 pkgs/applications/science/biology/mni_autoreg/default.nix diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix new file mode 100644 index 00000000000..5e7808918e9 --- /dev/null +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchgit, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: + +stdenv.mkDerivation rec { + pname = "mni_autoreg"; + name = "${pname}-0.99.70"; + + src = fetchgit { + url = "https://github.com/BIC-MNI/${pname}.git"; + rev = "a4367b82012fe3b40e794fc1eb6c3c86e86148bf"; + sha256 = "1j5vk7hf03y38fwb5klfppk3g4d2hx1fg3ikph2708pnssmim2qr"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc ]; + propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${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 : $PERL5LIB; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/mni_autoreg; + description = "Tools for automated registration using the MINC image format"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + }; +} + diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index d16043ce274..ba3d6192a21 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19765,6 +19765,10 @@ with pkgs; inherit (perlPackages) TextFormat; }; + mni_autoreg = callPackage ../applications/science/biology/mni_autoreg { + inherit (perlPackages) GetoptTabular MNI-Perllib; + }; + ncbi_tools = callPackage ../applications/science/biology/ncbi-tools { }; paml = callPackage ../applications/science/biology/paml { }; From f532f9f5f4d79a0ce3d2903ab9cd0dc7cfaa6aec Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 25 Sep 2017 12:17:49 -0400 Subject: [PATCH 07/22] minc-widgets: init at "1.0.0" (package seems to lack a consistent version) --- .../science/biology/minc-widgets/default.nix | 33 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 +++ 2 files changed, 37 insertions(+) create mode 100644 pkgs/applications/science/biology/minc-widgets/default.nix diff --git a/pkgs/applications/science/biology/minc-widgets/default.nix b/pkgs/applications/science/biology/minc-widgets/default.nix new file mode 100644 index 00000000000..0474ad1bff0 --- /dev/null +++ b/pkgs/applications/science/biology/minc-widgets/default.nix @@ -0,0 +1,33 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, GetoptTabular, MNI-Perllib, + libminc, octave, coreutils, minc_tools }: + +stdenv.mkDerivation rec { + pname = "minc-widgets"; + name = "${pname}-1.0.0"; + + + 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/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index ba3d6192a21..056b35f1426 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19765,6 +19765,10 @@ with pkgs; inherit (perlPackages) TextFormat; }; + minc_widgets = callPackage ../applications/science/biology/minc-widgets { + inherit (perlPackages) GetoptTabular MNI-Perllib; + }; + mni_autoreg = callPackage ../applications/science/biology/mni_autoreg { inherit (perlPackages) GetoptTabular MNI-Perllib; }; From 54c543b03b60bdd78bcfe86aab6784a2a54bd68e Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 25 Sep 2017 13:14:59 -0400 Subject: [PATCH 08/22] n3: init at 1.0.20 --- .../science/biology/N3/default.nix | 37 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 ++ 2 files changed, 41 insertions(+) create mode 100644 pkgs/applications/science/biology/N3/default.nix diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix new file mode 100644 index 00000000000..feaea5b1534 --- /dev/null +++ b/pkgs/applications/science/biology/N3/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, MNI-Perllib, GetoptTabular, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "N3"; + name = "${pname}-1.0.20"; + + 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; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 056b35f1426..51edd6d16e0 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19749,6 +19749,10 @@ 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; }; From e90d1e8631d62053b9f16343baececda9e92406f Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 25 Sep 2017 14:20:56 -0400 Subject: [PATCH 09/22] inormalize: init at 1.0.20 (develop branch) --- .../science/biology/inormalize/default.nix | 38 +++++++++++++++++++ .../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 00000000000..d202db8521c --- /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 00000000000..953bce9a184 --- /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 00000000000..75dc46a799c --- /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 51edd6d16e0..cd34788fc39 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; }; From cf2aac6a045f97a20b79978693547ea83abc076a Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 26 Sep 2017 13:22:46 -0400 Subject: [PATCH 10/22] address license/version issues for PR #29782 --- pkgs/applications/science/biology/N3/default.nix | 3 ++- .../science/biology/inormalize/default.nix | 3 ++- .../science/biology/minc-tools/default.nix | 3 ++- .../science/biology/minc-widgets/default.nix | 3 ++- .../science/biology/mni_autoreg/default.nix | 14 ++++++++------ pkgs/development/libraries/libminc/default.nix | 11 +++++++---- .../libraries/science/biology/EBTKS/default.nix | 5 +++-- pkgs/development/perl-modules/MNI/default.nix | 7 ++++--- pkgs/top-level/perl-packages.nix | 1 + 9 files changed, 31 insertions(+), 19 deletions(-) diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix index feaea5b1534..c14846beec2 100644 --- a/pkgs/applications/science/biology/N3/default.nix +++ b/pkgs/applications/science/biology/N3/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "N3"; - name = "${pname}-1.0.20"; + name = "${pname}-2017-09-18"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -33,5 +33,6 @@ stdenv.mkDerivation rec { 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 index d202db8521c..f17143ad06b 100644 --- a/pkgs/applications/science/biology/inormalize/default.nix +++ b/pkgs/applications/science/biology/inormalize/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "inormalize"; - name = "${pname}-1.0.20"; + name = "${pname}-2014-10-21"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -34,5 +34,6 @@ stdenv.mkDerivation rec { 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/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 011db3f0fb8..8e1f74686d1 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "minc-tools"; - name = "${pname}-2.3.01"; + name = "${pname}-2017-09-11"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -32,5 +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 index 0474ad1bff0..9084dfb2e1c 100644 --- a/pkgs/applications/science/biology/minc-widgets/default.nix +++ b/pkgs/applications/science/biology/minc-widgets/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "minc-widgets"; - name = "${pname}-1.0.0"; + name = "${pname}-2016-04-20"; src = fetchFromGitHub { @@ -29,5 +29,6 @@ stdenv.mkDerivation rec { 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 index 5e7808918e9..076ecd03a1b 100644 --- a/pkgs/applications/science/biology/mni_autoreg/default.nix +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -1,13 +1,14 @@ -{ stdenv, fetchgit, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: +{ stdenv, fetchFromGitHub, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: stdenv.mkDerivation rec { pname = "mni_autoreg"; - name = "${pname}-0.99.70"; + name = "${pname}-2017-09-22"; - src = fetchgit { - url = "https://github.com/BIC-MNI/${pname}.git"; - rev = "a4367b82012fe3b40e794fc1eb6c3c86e86148bf"; - sha256 = "1j5vk7hf03y38fwb5klfppk3g4d2hx1fg3ikph2708pnssmim2qr"; + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "ab99e29987dc029737785baebf24896ec37a2d76"; + sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq"; }; nativeBuildInputs = [ cmake makeWrapper ]; @@ -29,6 +30,7 @@ stdenv.mkDerivation rec { description = "Tools for automated registration using the MINC image format"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + license = licenses.free; }; } diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix index e133e4be01c..971741a019c 100644 --- a/pkgs/development/libraries/libminc/default.nix +++ b/pkgs/development/libraries/libminc/default.nix @@ -2,11 +2,13 @@ stdenv.mkDerivation rec { pname = "libminc"; - name = "${pname}-2.3.01"; + name = "${pname}-2017-09-14"; - # current master significantly ahead of most recent release + owner = "BIC-MNI"; + + # current master is significantly ahead of most recent release, so use Git version: src = fetchFromGitHub { - owner = "BIC-MNI"; + inherit owner; repo = pname; rev = "e11c6df9321b4061bf87a7d43171ec55e9e3908f"; sha256 = "0lmd0js3jgni2mw1zfvd4qg6byxiv3ndgv2z3nm7975i83zw48xk"; @@ -30,9 +32,10 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with stdenv.lib; { - homepage = https://github.com/BIC-MNI/libminc; + homepage = "https://github.com/${owner}/${pname}"; description = "Medical imaging library based on HDF5"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + license = licenses.free; }; } diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix index 3103eb31fb8..6ed6c8262a5 100644 --- a/pkgs/development/libraries/science/biology/EBTKS/default.nix +++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -14,14 +14,15 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ libminc ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; - checkPhase = "ctest --output-on-failure"; # but there are no tests ... + checkPhase = "ctest --output-on-failure"; # but cmake doesn't run the tests ... meta = with stdenv.lib; { homepage = "https://github.com/BIC-MNI/${pname}"; description = "Library for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + licenses = licenses.free; }; } diff --git a/pkgs/development/perl-modules/MNI/default.nix b/pkgs/development/perl-modules/MNI/default.nix index 806c7703c88..50a2d71ad22 100644 --- a/pkgs/development/perl-modules/MNI/default.nix +++ b/pkgs/development/perl-modules/MNI/default.nix @@ -1,7 +1,7 @@ { fetchFromGitHub, buildPerlPackage, stdenv, perl }: buildPerlPackage rec { - name = "MNI-Perllib-0.08"; + name = "MNI-Perllib-2012-04-13"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -14,7 +14,8 @@ buildPerlPackage rec { doCheck = false; # TODO: almost all tests fail ... is this a real problem? - meta = { - license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ]; + meta = with stdenv.lib; { + license = with licenses; [ artistic1 gpl1Plus ]; + maintainer = with maintainers; [ bcdarwin ]; }; } diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index c34986db385..d67a3f7f1dd 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -15012,6 +15012,7 @@ let self = _self // overrides; _self = with self; { homepage = http://www.shlomifish.org/open-source/projects/Text-Format/; description = "Format text"; license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ]; + maintainer = with maintainers; [ bcdarwin ]; }; }; From c14342d44fa000773bcb9a6f092d2c703b294b1f Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 26 Sep 2017 17:59:53 -0400 Subject: [PATCH 11/22] itk: enable more MINC support --- pkgs/development/libraries/itk/default.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/development/libraries/itk/default.nix b/pkgs/development/libraries/itk/default.nix index 10c160eacc6..5280a95afb4 100644 --- a/pkgs/development/libraries/itk/default.nix +++ b/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" ]; From c9db4cabc8e5e630a5fc9e3533c3954370907139 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 26 Sep 2017 18:03:47 -0400 Subject: [PATCH 12/22] bicpl: init at 2017-09-10 --- .../science/biology/bicpl/default.nix | 33 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 35 insertions(+) create mode 100644 pkgs/development/libraries/science/biology/bicpl/default.nix diff --git a/pkgs/development/libraries/science/biology/bicpl/default.nix b/pkgs/development/libraries/science/biology/bicpl/default.nix new file mode 100644 index 00000000000..d00a74f61e2 --- /dev/null +++ b/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; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index cd34788fc39..f74a9b75f5e 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -8469,6 +8469,8 @@ 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; From de2f36982bd22053d0686dbec6aa8a7fe5fddfcb Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 26 Sep 2017 18:08:14 -0400 Subject: [PATCH 13/22] ezminc: init at 2017-08-29 --- .../science/biology/EZminc/default.nix | 32 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 34 insertions(+) create mode 100644 pkgs/applications/science/biology/EZminc/default.nix diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix new file mode 100644 index 00000000000..20d88eb3aaf --- /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/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index f74a9b75f5e..c5faf48dda8 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19739,6 +19739,8 @@ with pkgs; emboss = callPackage ../applications/science/biology/emboss { }; + ezminc = callPackage ../applications/science/biology/EZminc { }; + htslib = callPackage ../development/libraries/science/biology/htslib { }; igv = callPackage ../applications/science/biology/igv { }; From d094f52112e3ffa75d5d9371fbeca804bd0200c9 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 26 Sep 2017 23:50:51 -0400 Subject: [PATCH 14/22] fix EBTKS version naming --- pkgs/development/libraries/science/biology/EBTKS/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix index 6ed6c8262a5..9e27d041f8d 100644 --- a/pkgs/development/libraries/science/biology/EBTKS/default.nix +++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "EBTKS"; - name = "${pname}-1.6.50"; + name = "${pname}-2017-09-23"; src = fetchFromGitHub { owner = "BIC-MNI"; From 6972e366beb9c6b25567ed0d5378193301a73ef5 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Fri, 29 Sep 2017 14:03:25 -0400 Subject: [PATCH 15/22] arguments: init at 2015-11-30 --- .../libraries/arguments/default.nix | 32 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 34 insertions(+) create mode 100644 pkgs/development/libraries/arguments/default.nix diff --git a/pkgs/development/libraries/arguments/default.nix b/pkgs/development/libraries/arguments/default.nix new file mode 100644 index 00000000000..912ea53c3d3 --- /dev/null +++ b/pkgs/development/libraries/arguments/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, libminc, bicpl }: + +stdenv.mkDerivation rec { + pname = "arguments"; + name = "${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; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index c5faf48dda8..944abb463cc 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -517,6 +517,8 @@ 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 {}; From c1488921a03d6e4119934169e941438bc4e1da39 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Fri, 29 Sep 2017 14:04:05 -0400 Subject: [PATCH 16/22] oobicpl: init at 2016-03-02 --- .../science/biology/oobicpl/default.nix | 31 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 33 insertions(+) create mode 100644 pkgs/development/libraries/science/biology/oobicpl/default.nix diff --git a/pkgs/development/libraries/science/biology/oobicpl/default.nix b/pkgs/development/libraries/science/biology/oobicpl/default.nix new file mode 100644 index 00000000000..8755b7fd2eb --- /dev/null +++ b/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; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 944abb463cc..ec9c00a7a79 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -10787,6 +10787,8 @@ with pkgs; oniguruma = callPackage ../development/libraries/oniguruma { }; + oobicpl = callPackage ../development/libraries/science/biology/oobicpl { }; + openal = self.openalSoft; openalSoft = callPackage ../development/libraries/openal-soft { From 524b606f16ac59e1877e2e62994b7752c0b7206a Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 9 Apr 2018 20:29:03 -0400 Subject: [PATCH 17/22] disable a second libminc test --- pkgs/development/libraries/libminc/default.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix index 971741a019c..704c73284ae 100644 --- a/pkgs/development/libraries/libminc/default.nix +++ b/pkgs/development/libraries/libminc/default.nix @@ -25,7 +25,8 @@ stdenv.mkDerivation rec { checkPhase = '' export LD_LIBRARY_PATH="$(pwd)" # see #22060 - ctest -E ezminc_rw_test --output-on-failure # ezminc_rw_test can't find libminc_io.so.5.2.0 + 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; From 1595f3cc454ccd859281b244710b6a084c2c646c Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 9 Apr 2018 20:29:29 -0400 Subject: [PATCH 18/22] delete broken alias --- pkgs/top-level/aliases.nix | 1 - 1 file changed, 1 deletion(-) diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix index c6a9825a1d6..4a169c69295 100644 --- a/pkgs/top-level/aliases.nix +++ b/pkgs/top-level/aliases.nix @@ -133,7 +133,6 @@ 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 From 12fa2f9fd37eaf0c12de0d2ef75e93a05d9788a4 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Mon, 9 Apr 2018 23:52:18 -0400 Subject: [PATCH 19/22] metadata fixes: EBTKS, MNI::Perllib, Text::Format --- pkgs/development/libraries/science/biology/EBTKS/default.nix | 2 +- pkgs/development/perl-modules/MNI/default.nix | 2 +- pkgs/top-level/perl-packages.nix | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix index 9e27d041f8d..67f868a91a7 100644 --- a/pkgs/development/libraries/science/biology/EBTKS/default.nix +++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -23,6 +23,6 @@ stdenv.mkDerivation rec { description = "Library for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; - licenses = licenses.free; + license = licenses.free; }; } diff --git a/pkgs/development/perl-modules/MNI/default.nix b/pkgs/development/perl-modules/MNI/default.nix index 50a2d71ad22..176cd06a9cc 100644 --- a/pkgs/development/perl-modules/MNI/default.nix +++ b/pkgs/development/perl-modules/MNI/default.nix @@ -16,6 +16,6 @@ buildPerlPackage rec { meta = with stdenv.lib; { license = with licenses; [ artistic1 gpl1Plus ]; - maintainer = with maintainers; [ bcdarwin ]; + maintainers = with maintainers; [ bcdarwin ]; }; } diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index d67a3f7f1dd..0d2df26e050 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -15012,7 +15012,7 @@ let self = _self // overrides; _self = with self; { homepage = http://www.shlomifish.org/open-source/projects/Text-Format/; description = "Format text"; license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ]; - maintainer = with maintainers; [ bcdarwin ]; + maintainers = with maintainers; [ bcdarwin ]; }; }; From efb02d3c00bf7852263daadb1f5c6207da52a705 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 10 Apr 2018 13:34:29 -0400 Subject: [PATCH 20/22] elastix: 4.8 -> 4.9.0 --- .../science/biology/elastix/default.nix | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix index 06550372ba8..7b9e6b24d41 100644 --- a/pkgs/development/libraries/science/biology/elastix/default.nix +++ b/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/${pversion}.tar.gz"; + sha256 = "02pbln36nq98xxfyqwlxg7b6gmigdq4fgfqr9mym1qn58aj04shg"; }; nativeBuildInputs = [ cmake python ]; buildInputs = [ itk ]; - cmakeFlags = [ "-DUSE_KNNGraphAlphaMutualInformationMetric=OFF" ]; - checkPhase = "ctest"; meta = with stdenv.lib; { From 6908f0ce89cd3dd9fa4b3c8f5ee10f2bd9895817 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Tue, 10 Apr 2018 13:38:14 -0400 Subject: [PATCH 21/22] c3d: updated rev still won't compile; mark broken --- pkgs/applications/graphics/c3d/default.nix | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/graphics/c3d/default.nix b/pkgs/applications/graphics/c3d/default.nix index 74631e88ebf..7e1c6d7c8c4 100644 --- a/pkgs/applications/graphics/c3d/default.nix +++ b/pkgs/applications/graphics/c3d/default.nix @@ -3,12 +3,12 @@ stdenv.mkDerivation rec { name = "${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; }; } From b1d4962d67ec7db912f6647764097e637a9dddee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Sat, 21 Apr 2018 20:23:15 +0100 Subject: [PATCH 22/22] perlPackages.MNI-Perllib: use callPackage instead of import --- pkgs/top-level/perl-packages.nix | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index e60a4b84758..e9d6cd97bc8 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -9634,9 +9634,7 @@ let self = _self // overrides; _self = with self; { }; }; - MNI-Perllib = import ../development/perl-modules/MNI { - inherit buildPerlPackage fetchFromGitHub stdenv perl; - }; + MNI-Perllib = pkgs.callPackage ../development/perl-modules/MNI {}; Mo = buildPerlPackage rec { name = "Mo-0.40"; @@ -16254,7 +16252,8 @@ let self = _self // overrides; _self = with self; { license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ]; maintainers = with maintainers; [ bcdarwin ]; }; - + }; + TextGerman = buildPerlPackage rec { name = "Text-German-0.06"; src = fetchurl {