diff options
Diffstat (limited to 'nixpkgs/pkgs/development/libraries/science/biology')
13 files changed, 443 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix new file mode 100644 index 000000000000..b75ac06627fb --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -0,0 +1,26 @@ +{ lib, 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/cmake" ]; + + meta = with lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Library for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix new file mode 100644 index 000000000000..bc2de6e882f9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix @@ -0,0 +1,31 @@ +{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }: + +stdenv.mkDerivation rec { + pname = "bicgl"; + version = "unstable-2018-04-06"; + + owner = "BIC-MNI"; + + src = fetchFromGitHub { + inherit owner; + repo = pname; + rev = "61a035751c9244fcca1edf94d6566fa2a709ce90"; + sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc bicpl freeglut mesa_glu ]; + + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DBICPL_DIR=${bicpl}/lib" + ]; + + meta = with lib; { + homepage = "https://github.com/${owner}/${pname}"; + description = "Brain Imaging Centre graphics library"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix new file mode 100644 index 000000000000..0bdcbf5a828a --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix @@ -0,0 +1,32 @@ +{ lib, stdenv, fetchFromGitHub, cmake, libminc, netpbm }: + +stdenv.mkDerivation rec { + pname = "bicpl"; + version = "unstable-2017-09-10"; + + owner = "BIC-MNI"; + + # current master is significantly ahead of most recent release, so use Git version: + src = fetchFromGitHub { + inherit owner; + repo = pname; + rev = "612a63e740fadb162fcf27ee00da6a18dec4d5a9"; + sha256 = "1vv9gi184bkvp3f99v9xmmw1ly63ip5b09y7zdjn39g7kmwzrga7"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc netpbm ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ]; + + doCheck = false; + # internal_volume_io.h: No such file or directory + + meta = with 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/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix new file mode 100644 index 000000000000..d1eb096e08e6 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix @@ -0,0 +1,36 @@ +{ lib, stdenv, fetchFromGitHub, cmake }: + +stdenv.mkDerivation rec { + pname = "bpp-core"; + version = "2.4.1"; + + src = fetchFromGitHub { owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"; + }; + + nativeBuildInputs = [ cmake ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/bpp-core/bpp-core-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = with lib; { + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Main_Page"; + changelog = "https://github.com/BioPP/bpp-core/blob/master/ChangeLog"; + description = "C++ bioinformatics libraries and tools"; + maintainers = with maintainers; [ bcdarwin ]; + license = licenses.cecill20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix new file mode 100644 index 000000000000..8ff6ad433fb5 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-phyl/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-phyl"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bpp-phyl/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix new file mode 100644 index 000000000000..af5d1d00d4d9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-popgen/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-popgen"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bpp-popgen/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix new file mode 100644 index 000000000000..ef3f3d5756e9 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core }: + +stdenv.mkDerivation rec { + pname = "bpp-seq"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bpp-seq/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix new file mode 100644 index 000000000000..55ee5ab4fb66 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix @@ -0,0 +1,38 @@ +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3, Cocoa }: + +stdenv.mkDerivation rec { + pname = "elastix"; + version = "5.0.1"; + + src = fetchFromGitHub { + owner = "SuperElastix"; + repo = pname; + rev = version; + sha256 = "1mx8kkak2d3ibfrxrh8jkmh2zkdlgl9h578wiw3617zcwaa97bxw"; + }; + + patches = [ + (fetchpatch { + name = "install-executables.patch"; # https://github.com/SuperElastix/elastix/issues/305 + url = "https://github.com/SuperElastix/elastix/commit/8e26cdc0d66f6030c7be085fdc424d84d4fc7546.patch"; + sha256 = "12y9wbpi9jlarnw6fk4iby97jxvx5g4daq9zqblbcmn51r134bj5"; + }) + ]; + + nativeBuildInputs = [ cmake python3 ]; + buildInputs = [ itk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; + + doCheck = !stdenv.isDarwin; # usual dynamic linker issues + + preCheck = " + export LD_LIBRARY_PATH=$(pwd)/bin + "; + + meta = with lib; { + homepage = "http://elastix.isi.uu.nl/"; + description = "Image registration toolkit based on ITK"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.x86_64; # libitkpng linker issues with ITK 5.1 + license = licenses.asl20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix new file mode 100644 index 000000000000..306324129cbd --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix @@ -0,0 +1,34 @@ +{ lib, stdenv, fetchFromGitHub, cmake, expat, nifticlib, zlib }: + +stdenv.mkDerivation rec { + pname = "gifticlib"; + version = "unstable-2020-07-07"; + + src = fetchFromGitHub { + owner = "NIFTI-Imaging"; + repo = "gifti_clib"; + rev = "5eae81ba1e87ef3553df3b6ba585f12dc81a0030"; + sha256 = "0gcab06gm0irjnlrkpszzd4wr8z0fi7gx8f7966gywdp2jlxzw19"; + }; + + cmakeFlags = [ "-DUSE_SYSTEM_NIFTI=ON" "-DDOWNLOAD_TEST_DATA=OFF" ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ expat nifticlib zlib ]; + + # without the test data, this is only a few basic tests + doCheck = !stdenv.isDarwin; + checkPhase = '' + runHook preCheck + ctest -LE 'NEEDS_DATA' + runHook postCheck + ''; + + meta = with lib; { + homepage = "https://www.nitrc.org/projects/gifti"; + description = "Medical imaging geometry format C API"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.publicDomain; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix new file mode 100644 index 000000000000..cb3a543ad2af --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix @@ -0,0 +1,36 @@ +{ lib, stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }: + +stdenv.mkDerivation rec { + pname = "htslib"; + version = "1.11"; + + src = fetchurl { + url = "https://github.com/samtools/htslib/releases/download/${version}/${pname}-${version}.tar.bz2"; + sha256 = "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"; + }; + + # perl is only used during the check phase. + nativeBuildInputs = [ perl ]; + + buildInputs = [ zlib bzip2 lzma curl ]; + + configureFlags = [ "--enable-libcurl" ]; # optional but strongly recommended + + installFlags = [ "prefix=$(out)" ]; + + preCheck = '' + patchShebangs test/ + ''; + + enableParallelBuilding = true; + + doCheck = true; + + meta = with lib; { + description = "A C library for reading/writing high-throughput sequencing data"; + license = licenses.mit; + homepage = "http://www.htslib.org/"; + platforms = platforms.unix; + maintainers = [ maintainers.mimame ]; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix new file mode 100644 index 000000000000..0d23489696f1 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix @@ -0,0 +1,44 @@ +{ lib, stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python, vtk, zlib, tbb }: + +stdenv.mkDerivation rec { + version = "2.0.0"; + pname = "mirtk"; + + src = fetchFromGitHub { + owner = "BioMedIA"; + repo = "MIRTK"; + rev = "v${version}"; + sha256 = "0i2v97m66ir5myvi5b123r7zcagwy551b73s984gk7lksl5yiqxk"; + fetchSubmodules = true; + }; + + cmakeFlags = [ + "-DWITH_VTK=ON" + "-DBUILD_ALL_MODULES=ON" + "-DWITH_TBB=ON" + ]; + + doCheck = true; + + checkPhase = '' + ctest -E '(Polynomial|ConvolutionFunction|Downsampling|EdgeTable|InterpolateExtrapolateImage)' + ''; + # testPolynomial - segfaults for some reason + # testConvolutionFunction, testDownsampling - main not called correctly + # testEdgeTable, testInterpolateExtrapolateImageFunction - setup fails + + postInstall = '' + install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk + ''; + + nativeBuildInputs = [ cmake gtest ]; + buildInputs = [ boost eigen python vtk zlib tbb ]; + + meta = with lib; { + homepage = "https://github.com/BioMedIA/MIRTK"; + description = "Medical image registration library and tools"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.linux; + license = licenses.asl20; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix new file mode 100644 index 000000000000..fee2ea8772b4 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix @@ -0,0 +1,33 @@ +{ lib, stdenv, fetchFromGitHub, cmake, zlib }: + +stdenv.mkDerivation rec { + pname = "nifticlib"; + version = "3.0.1"; + + src = fetchFromGitHub { + owner = "NIFTI-Imaging"; + repo = "nifti_clib"; + rev = "v${version}"; + sha256 = "0hamm6nvbjdjjd5md4jahzvn5559frigxaiybnjkh59ckxwb1hy4"; + }; + + cmakeFlags = [ "-DDOWNLOAD_TEST_DATA=OFF" ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib ]; + + checkPhase = '' + runHook preCheck + ctest -LE 'NEEDS_DATA' + runHook postCheck + ''; + doCheck = true; + + meta = with lib; { + homepage = "https://nifti-imaging.github.io"; + description = "Medical imaging format C API"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.publicDomain; + }; +} diff --git a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix new file mode 100644 index 000000000000..626e6475ba18 --- /dev/null +++ b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix @@ -0,0 +1,31 @@ +{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }: + +stdenv.mkDerivation rec { + pname = "oobicpl"; + version = "unstable-2016-03-02"; + + owner = "BIC-MNI"; + + src = fetchFromGitHub { + inherit owner; + repo = pname; + rev = "bc062a65dead2e58461f5afb37abedfa6173f10c"; + sha256 = "05l4ml9djw17bgdnrldhcxydrzkr2f2scqlyak52ph5azj5n4zsx"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ libminc bicpl arguments pcre-cpp ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DBICPL_DIR=${bicpl}/lib" + "-DARGUMENTS_DIR=${arguments}/lib" + "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ]; + + meta = with 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; + }; +} |