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; }; } 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/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix new file mode 100644 index 00000000000..c14846beec2 --- /dev/null +++ b/pkgs/applications/science/biology/N3/default.nix @@ -0,0 +1,38 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, MNI-Perllib, GetoptTabular, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "N3"; + name = "${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 00000000000..f17143ad06b --- /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 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/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 7864658c958..8e1f74686d1 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 : $PERL5LIB + done + ''; enableParallelBuilding = true; @@ -26,5 +32,6 @@ stdenv.mkDerivation rec { description = "Command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + license = licenses.free; }; } diff --git a/pkgs/applications/science/biology/minc-widgets/default.nix b/pkgs/applications/science/biology/minc-widgets/default.nix new file mode 100644 index 00000000000..9084dfb2e1c --- /dev/null +++ b/pkgs/applications/science/biology/minc-widgets/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perl, GetoptTabular, MNI-Perllib, + libminc, octave, coreutils, minc_tools }: + +stdenv.mkDerivation rec { + pname = "minc-widgets"; + name = "${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/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix new file mode 100644 index 00000000000..076ecd03a1b --- /dev/null +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: + +stdenv.mkDerivation rec { + pname = "mni_autoreg"; + name = "${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 : $PERL5LIB; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/mni_autoreg; + description = "Tools for automated registration using the MINC image format"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} + diff --git a/pkgs/development/libraries/arguments/default.nix b/pkgs/development/libraries/arguments/default.nix new file mode 100644 index 00000000000..912ea53c3d3 --- /dev/null +++ b/pkgs/development/libraries/arguments/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, libminc, bicpl }: + +stdenv.mkDerivation rec { + pname = "arguments"; + name = "${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/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" ]; diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix index 673b572c089..704c73284ae 100644 --- a/pkgs/development/libraries/libminc/default.nix +++ b/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}/${pname}"; description = "Medical imaging library based on HDF5"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; + license = licenses.free; }; } diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix new file mode 100644 index 00000000000..67f868a91a7 --- /dev/null +++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -0,0 +1,28 @@ +{ stdenv, fetchFromGitHub, cmake, libminc }: + +stdenv.mkDerivation rec { + pname = "EBTKS"; + name = "${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; + }; +} 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/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; { 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/development/perl-modules/MNI/default.nix b/pkgs/development/perl-modules/MNI/default.nix new file mode 100644 index 00000000000..176cd06a9cc --- /dev/null +++ b/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 ]; + }; +} 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/aliases.nix b/pkgs/top-level/aliases.nix index 9c3108913c6..4b4dd2bf915 100644 --- a/pkgs/top-level/aliases.nix +++ b/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 diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 11010ca097b..95d83af3aaf 100644 --- a/pkgs/top-level/all-packages.nix +++ b/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 { }; diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index da3f1d9e87a..e9d6cd97bc8 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/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 {