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Merge pull request #235322 from natsukium/dssp/update

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dssp: 4.2.2.1 -> 4.3.1; libcifpp: 5.0.8 -> 5.1.0.1; libmcfp: 1.2.3 -> 1.2.4
This commit is contained in:
Martin Weinelt 2023-07-02 23:12:49 +02:00 committed by GitHub
commit bb40b8c205
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3 changed files with 79 additions and 34 deletions
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43
pkgs/applications/science/biology/dssp/default.nix
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@ -1,36 +1,49 @@
{ lib, stdenv, fetchFromGitHub, cmake, libcifpp, libmcfp, zlib }:
{ lib
, stdenv
, cmake
, fetchFromGitHub
, libcifpp
, libmcfp
, zlib
}:
let
libcifpp' = libcifpp.overrideAttrs (oldAttrs: rec {
# dssp 4.2.2.1 requires specific version "5.0.8" of libcifpp
version = "5.0.8";
libcifpp' = libcifpp.overrideAttrs (oldAttrs: {
# dssp 4.3.1 requires specific version "5.1.0" of libcifpp
version = "5.1.0";
src = fetchFromGitHub {
inherit (oldAttrs.src) owner repo;
rev = "v${version}";
sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco=";
inherit (oldAttrs.src) owner repo rev;
hash = "sha256-PUsi4T6huSqwaa6RnBP1Vj+0a1ePrvrHD0641Lkkc5s=";
};
});
in
stdenv.mkDerivation rec {
stdenv.mkDerivation (finalAttrs: {
pname = "dssp";
version = "4.2.2.1";
version = "4.3.1";
src = fetchFromGitHub {
owner = "PDB-REDO";
repo = pname;
rev = "v${version}";
sha256 = "sha256-vmGvC5d8LTo+pcY9sxwj0d6JvH8Lyk+QSOZo5raBci4=";
repo = "dssp";
rev = "refs/tags/v${finalAttrs.version}";
hash = "sha256-TE2fus3KaGd9jo7cOWmJSooHjxTbcxEldR1Mui2SGP0=";
};
nativeBuildInputs = [ cmake ];
nativeBuildInputs = [
cmake
];
buildInputs = [ libcifpp' libmcfp zlib ];
buildInputs = [
libcifpp'
libmcfp
zlib
];
meta = with lib; {
description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein";
homepage = "https://github.com/PDB-REDO/dssp";
changelog = "https://github.com/PDB-REDO/libcifpp/releases/tag/${finalAttrs.src.rev}";
license = licenses.bsd2;
maintainers = with maintainers; [ natsukium ];
platforms = platforms.unix;
};
}
})

47
pkgs/development/libraries/libcifpp/default.nix
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@ -1,28 +1,53 @@
{ lib, stdenv, fetchFromGitHub, boost, cmake, zlib }:
{ lib
, stdenv
, boost
, cmake
, fetchFromGitHub
, fetchpatch
, eigen
, zlib
}:
stdenv.mkDerivation rec {
stdenv.mkDerivation (finalAttrs: {
pname = "libcifpp";
version = "5.0.8";
version = "5.1.0.1";
src = fetchFromGitHub {
owner = "PDB-REDO";
repo = pname;
rev = "v${version}";
sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco=";
repo = "libcifpp";
rev = "refs/tags/v${finalAttrs.version}";
hash = "sha256-fAH7FIgJuitPUoacLnLs8uf9di5iM0c/2WHZqVjJOUE=";
};
nativeBuildInputs = [ cmake ];
patches = [
(fetchpatch {
name = "add-include-compare.patch";
url = "https://github.com/PDB-REDO/libcifpp/commit/676c0c8dc87437e2096718fd8c0750b995e174ba.patch";
hash = "sha256-fbA4fgiTY93+hFct+BQuHF7uv2nG7D9PljQxq1CkReU=";
})
];
# disable network access
cmakeFlags = [ "-DCIFPP_DOWNLOAD_CCD=OFF" ];
nativeBuildInputs = [
cmake
];
buildInputs = [ boost zlib ];
cmakeFlags = [
# disable network access
"-DCIFPP_DOWNLOAD_CCD=OFF"
];
buildInputs = [
boost
eigen
zlib
];
meta = with lib; {
description = "Manipulate mmCIF and PDB files";
homepage = "https://github.com/PDB-REDO/libcifpp";
changelog = "https://github.com/PDB-REDO/libcifpp/releases/tag/${finalAttrs.src.rev}";
license = licenses.bsd2;
maintainers = with maintainers; [ natsukium ];
platforms = platforms.unix;
};
}
})

23
pkgs/development/libraries/libmcfp/default.nix
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@ -1,23 +1,30 @@
{ lib, stdenv, fetchFromGitHub, cmake }:
{ lib
, stdenv
, cmake
, fetchFromGitHub
}:
stdenv.mkDerivation rec {
stdenv.mkDerivation (finalAttrs: {
pname = "libmcfp";
version = "1.2.3";
version = "1.2.4";
src = fetchFromGitHub {
owner = "mhekkel";
repo = pname;
rev = "v${version}";
sha256 = "sha256-Mi5nj8vR1j3V7fIMBrSyhD57emmlkCb0F08+5s7Usj0=";
repo = "libmcfp";
rev = "refs/tags/v${finalAttrs.version}";
hash = "sha256-Xz7M3TmUHGqiYZbFGSDxsVvg4VhgoVvr9TW03UxdFBw=";
};
nativeBuildInputs = [ cmake ];
nativeBuildInputs = [
cmake
];
meta = with lib; {
description = "Header only library that can collect configuration options from command line arguments";
homepage = "https://github.com/mhekkel/libmcfp";
changelog = "https://github.com/mhekkel/libmcfp/blob/${finalAttrs.src.rev}/changelog";
license = licenses.bsd2;
maintainers = with maintainers; [ natsukium ];
platforms = platforms.unix;
};
}
})