pyrox.dev
Merge pull request #243431 from natsukium/kssd/update
kssd: 1.1 -> 2.21; enable aarch64-linux support
authored by OTABI Tomoya and committed by GitHub 9b586ea6 83b84c79
+34
-15
pkgs/applications/science/biology/kssd/default.nix
+34
-15
pkgs/applications/science/biology/kssd/default.nix
···
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{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }:
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stdenv.mkDerivation rec {
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pname = "kssd";
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version = "1.1";
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src = fetchFromGitHub {
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owner = "yhg926";
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repo = "public_kssd";
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rev = "v${version}";
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sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY=";
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};
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patches = [
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# Pull upstream patch for -fno-common toolchain support:
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# https://github.com/yhg926/public_kssd/pull/9
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(fetchpatch {
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name = "fno-common.patch";
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url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch";
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sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4=";
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})
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];
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nativeBuildInputs = [ autoconf automake ];
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buildInputs = [ zlib libtool ];
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installPhase = ''
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install -vD kssd $out/bin/kssd
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'';
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meta = with lib; {
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description = "K-mer substring space decomposition";
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license = licenses.asl20;
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homepage = "https://github.com/yhg926/public_kssd";
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maintainers = with maintainers; [ unode ];
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platforms = [ "x86_64-linux" ];
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};
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}
···
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{ lib
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, stdenv
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, fetchFromGitHub
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, fetchpatch
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, zlib
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, kssd
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, runCommand
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "kssd";
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version = "2.21";
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src = fetchFromGitHub {
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owner = "yhg926";
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repo = "public_kssd";
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rev = "v${finalAttrs.version}";
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hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w=";
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};
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patches = [
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# https://github.com/yhg926/public_kssd/pull/11
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(fetchpatch {
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name = "allocate-enough-memory.patch";
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url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch";
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hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM=";
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})
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];
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buildInputs = [ zlib ];
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installPhase = ''
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runHook preInstall
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install -vD kssd $out/bin/kssd
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runHook postInstall
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'';
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passthru.tests = {
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simple = runCommand "${finalAttrs.pname}-test" { } ''
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mkdir $out
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${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference
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${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2
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${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query
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'';
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};
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+
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meta = with lib; {
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description = "K-mer substring space decomposition";
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license = licenses.asl20;
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homepage = "https://github.com/yhg926/public_kssd";
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maintainers = with maintainers; [ unode ];
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platforms = platforms.linux;
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mainProgram = "kssd";
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};
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})