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Merge pull request #82180 from bcdarwin/bppcore

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bppsuite: init at 2.4.1
This commit is contained in:
Benjamin Hipple 2020-05-26 21:07:25 -04:00 committed by GitHub
commit f04a5af0cc
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6 changed files with 169 additions and 0 deletions
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21
pkgs/applications/science/biology/bppsuite/default.nix Normal file
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@ -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";
};
}

36
pkgs/development/libraries/science/biology/bpp-core/default.nix Normal file
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@ -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;
};
}

32
pkgs/development/libraries/science/biology/bpp-phyl/default.nix Normal file
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@ -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";
};
}

35
pkgs/development/libraries/science/biology/bpp-popgen/default.nix Normal file
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@ -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";
};
}

35
pkgs/development/libraries/science/biology/bpp-seq/default.nix Normal file
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@ -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";
};
}

10
pkgs/top-level/all-packages.nix
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@ -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 { };