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Merge pull request #243431 from natsukium/kssd/update

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kssd: 1.1 -> 2.21; enable aarch64-linux support
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OTABI Tomoya 2023-11-03 20:15:48 +09:00 committed by GitHub
commit 9b586ea68f
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1 changed files with 34 additions and 15 deletions
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49
pkgs/applications/science/biology/kssd/default.nix
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@ -1,38 +1,57 @@
{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }:
{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, zlib
, kssd
, runCommand
}:
stdenv.mkDerivation rec {
stdenv.mkDerivation (finalAttrs: {
pname = "kssd";
version = "1.1";
version = "2.21";
src = fetchFromGitHub {
owner = "yhg926";
repo = "public_kssd";
rev = "v${version}";
sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY=";
rev = "v${finalAttrs.version}";
hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w=";
};
patches = [
# Pull upstream patch for -fno-common toolchain support:
# https://github.com/yhg926/public_kssd/pull/9
# https://github.com/yhg926/public_kssd/pull/11
(fetchpatch {
name = "fno-common.patch";
url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch";
sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4=";
name = "allocate-enough-memory.patch";
url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch";
hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM=";
})
];
nativeBuildInputs = [ autoconf automake ];
buildInputs = [ zlib libtool ];
buildInputs = [ zlib ];
installPhase = ''
install -vD kssd $out/bin/kssd
runHook preInstall
install -vD kssd $out/bin/kssd
runHook postInstall
'';
passthru.tests = {
simple = runCommand "${finalAttrs.pname}-test" { } ''
mkdir $out
${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference
${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2
${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query
'';
};
meta = with lib; {
description = "K-mer substring space decomposition";
license = licenses.asl20;
homepage = "https://github.com/yhg926/public_kssd";
maintainers = with maintainers; [ unode ];
platforms = [ "x86_64-linux" ];
platforms = platforms.linux;
mainProgram = "kssd";
};
}
})