diff options
Diffstat (limited to 'pkgs')
6 files changed, 169 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/bppsuite/default.nix b/pkgs/applications/science/biology/bppsuite/default.nix new file mode 100644 index 000000000000..564a38708bcd --- /dev/null +++ b/pkgs/applications/science/biology/bppsuite/default.nix @@ -0,0 +1,21 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq, bpp-phyl, bpp-popgen }: + +stdenv.mkDerivation rec { + pname = "bppsuite"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq bpp-phyl bpp-popgen ]; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bppsuite/blob/master/ChangeLog"; + }; +} diff --git a/pkgs/development/libraries/science/biology/bpp-core/default.nix b/pkgs/development/libraries/science/biology/bpp-core/default.nix new file mode 100644 index 000000000000..cfbe19d724be --- /dev/null +++ b/pkgs/development/libraries/science/biology/bpp-core/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchFromGitHub, cmake }: + +stdenv.mkDerivation rec { + pname = "bpp-core"; + version = "2.4.1"; + + src = fetchFromGitHub { owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv"; + }; + + nativeBuildInputs = [ cmake ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/bpp-core/bpp-core-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = with stdenv.lib; { + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Main_Page"; + changelog = "https://github.com/BioPP/bpp-core/blob/master/ChangeLog"; + description = "C++ bioinformatics libraries and tools"; + maintainers = with maintainers; [ bcdarwin ]; + license = licenses.cecill20; + }; +} diff --git a/pkgs/development/libraries/science/biology/bpp-phyl/default.nix b/pkgs/development/libraries/science/biology/bpp-phyl/default.nix new file mode 100644 index 000000000000..8ff6ad433fb5 --- /dev/null +++ b/pkgs/development/libraries/science/biology/bpp-phyl/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-phyl"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bpp-phyl/blob/master/ChangeLog"; + }; +} diff --git a/pkgs/development/libraries/science/biology/bpp-popgen/default.nix b/pkgs/development/libraries/science/biology/bpp-popgen/default.nix new file mode 100644 index 000000000000..af5d1d00d4d9 --- /dev/null +++ b/pkgs/development/libraries/science/biology/bpp-popgen/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }: + +stdenv.mkDerivation rec { + pname = "bpp-popgen"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq ]; + + preCheck = '' + export LD_LIBRARY_PATH=$(pwd)/src + ''; + + postFixup = '' + substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake \ + --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX' + ''; + # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES + # of form /nix/store/.../nix/store/.../include, + # probably due to relative vs absolute path issue + + doCheck = !stdenv.isDarwin; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bpp-popgen/blob/master/ChangeLog"; + }; +} diff --git a/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/pkgs/development/libraries/science/biology/bpp-seq/default.nix new file mode 100644 index 000000000000..79fd0fe67716 --- /dev/null +++ b/pkgs/development/libraries/science/biology/bpp-seq/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core }: + +stdenv.mkDerivation rec { + pname = "bpp-seq"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${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/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 7598eecbae70..7c9f2dd9e304 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -24495,6 +24495,16 @@ in inherit (darwin.apple_sdk.frameworks) ApplicationServices; }; + bpp-core = callPackage ../development/libraries/science/biology/bpp-core { }; + + bpp-phyl = callPackage ../development/libraries/science/biology/bpp-phyl { }; + + bpp-popgen = callPackage ../development/libraries/science/biology/bpp-popgen { }; + + bpp-seq = callPackage ../development/libraries/science/biology/bpp-seq { }; + + bppsuite = callPackage ../applications/science/biology/bppsuite { }; + cd-hit = callPackage ../applications/science/biology/cd-hit { }; cmtk = callPackage ../applications/science/biology/cmtk { }; |