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spades: 3.15.5 -> 4.0.0

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Release: https://github.com/ablab/spades/releases/tag/v4.0.0
This commit is contained in:
Bruno Bzeznik 2024-06-17 12:07:02 +02:00
parent 116b140bab
commit 02e1e6f581
1 changed files with 40 additions and 12 deletions
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52
pkgs/by-name/sp/spades/package.nix
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@ -1,46 +1,74 @@
{
lib,
stdenv,
fetchurl,
zlib,
bzip2,
cmake,
fetchFromGitHub,
fetchpatch,
ncurses,
python3,
readline,
}:
stdenv.mkDerivation (finalAttrs: {
pname = "spades";
version = "3.15.5";
version = "4.0.0";
src = fetchurl {
url = "https://github.com/ablab/spades/releases/download/v${finalAttrs.version}/SPAdes-${finalAttrs.version}.tar.gz";
hash = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";
src = fetchFromGitHub {
owner = "ablab";
repo = "spades";
rev = "v${finalAttrs.version}";
hash = "sha256-k2+ddJIgGE41KGZODovU9VdurbWerEtdqNrFDwyuFjo=";
};
sourceRoot = "SPAdes-${finalAttrs.version}/src";
env.CXXFLAGS = toString [
# GCC 13: error: 'uint32_t' does not name a type
"-include cstdint"
sourceRoot = "source/src";
patches = [
# https://github.com/ablab/spades/pull/1314
(fetchpatch {
name = "copytree.patch";
url = "https://github.com/ablab/spades/commit/af1f756a46c5da669897b841d4f753af1eaa9588.patch";
hash = "sha256-tkT7hb0TqsbLkcTs9u43nzvV8bVdh3G9VKYqFFLrQv8=";
stripLen = 3;
extraPrefix = "projects/";
})
];
cmakeFlags = [
"-DZLIB_ENABLE_TESTS=OFF"
"-DSPADES_BUILD_INTERNAL=OFF"
];
preConfigure = ''
# The CMakeListsInternal.txt file should be empty in the release tarball
echo "" > CMakeListsInternal.txt
'';
nativeBuildInputs = [ cmake ];
buildInputs = [
zlib
bzip2
ncurses
python3
readline
];
doCheck = true;
strictDeps = true;
meta = {
description = "St. Petersburg genome assembler, a toolkit for assembling and analyzing sequencing data";
license = lib.licenses.gpl2Only;
changelog = "https://github.com/ablab/spades/blob/${finalAttrs.version}/changelog.md";
downloadPage = "https://github.com/ablab/spades";
homepage = "http://ablab.github.io/spades";
license = lib.licenses.gpl2Only;
platforms = [
"aarch64-linux"
"x86_64-linux"
"x86_64-darwin"
];
maintainers = with lib.maintainers; [ bzizou ];
broken = stdenv.hostPlatform.isMusl;
};
})