75 lines
1.8 KiB
Nix
75 lines
1.8 KiB
Nix
|
{
|
||
|
|
lib,
|
||
|
|
stdenv,
|
||
|
|
fetchFromGitHub,
|
||
|
|
boost,
|
||
|
|
gtest,
|
||
|
|
zlib,
|
||
|
|
}:
|
||
|
|
|
||
|
|
stdenv.mkDerivation (finalAttrs: {
|
||
|
|
pname = "dragmap";
|
||
|
|
version = "1.3.0";
|
||
|
|
|
||
|
|
src = fetchFromGitHub {
|
||
|
|
owner = "Illumina";
|
||
|
|
repo = "DRAGMAP";
|
||
|
|
tag = finalAttrs.version;
|
||
|
|
fetchSubmodules = true;
|
||
|
|
hash = "sha256-f1jsOErriS1I/iUS4CzJ3+Dz8SMUve/ccb3KaE+L7U8=";
|
||
|
|
};
|
||
|
|
|
||
|
|
nativebuildInputs = [ boost ];
|
||
|
|
buildInputs = [
|
||
|
|
gtest
|
||
|
|
zlib
|
||
|
|
];
|
||
|
|
|
||
|
|
patches = [
|
||
|
|
# pclose is called on a NULL value. This is no longer allowed since
|
||
|
|
# https://github.com/bminor/glibc/commit/64b1a44183a3094672ed304532bedb9acc707554
|
||
|
|
./stdio-pclose.patch
|
||
|
|
|
||
|
|
# Add missing include cstdint. Upstream does not accept PR. Issue opened at
|
||
|
|
# https://github.com/Illumina/DRAGMAP/issues/63
|
||
|
|
./cstdint.patch
|
||
|
|
|
||
|
|
# Missing import in Mapper.cpp
|
||
|
|
# Issue opened upstream https://github.com/Illumina/DRAGMAP/pull/66
|
||
|
|
./boost-iterator-range.patch
|
||
|
|
];
|
||
|
|
|
||
|
|
env = {
|
||
|
|
GTEST_INCLUDEDIR = "${gtest.dev}/include";
|
||
|
|
CPPFLAGS = "-I ${boost.dev}/include";
|
||
|
|
LDFLAGS = "-L ${boost.out}/lib";
|
||
|
|
};
|
||
|
|
|
||
|
|
installPhase = ''
|
||
|
|
runHook preInstall
|
||
|
|
|
||
|
|
mkdir -p $out/bin
|
||
|
|
cp build/release/dragen-os $out/bin/
|
||
|
|
|
||
|
|
runHook postInstall
|
||
|
|
'';
|
||
|
|
|
||
|
|
# Tests are launched by default from makefile
|
||
|
|
doCheck = false;
|
||
|
|
|
||
|
|
meta = {
|
||
|
|
description = "Open Source version of Dragen mapper for genomics";
|
||
|
|
mainProgram = "dragen-os";
|
||
|
|
longDescription = ''
|
||
|
|
DRAGMAP is an open-source software implementation of the DRAGEN mapper,
|
||
|
|
which the Illumina team created to procude the same results as their
|
||
|
|
proprietary DRAGEN hardware.
|
||
|
|
'';
|
||
|
|
homepage = "https://github.com/Illumina/DRAGMAP";
|
||
|
|
changelog = "https://github.com/Illumina/DRAGMAP/releases/tag/${finalAttrs.version}";
|
||
|
|
license = lib.licenses.gpl3;
|
||
|
|
platforms = [ "x86_64-linux" ];
|
||
|
|
maintainers = with lib.maintainers; [ apraga ];
|
||
|
|
};
|
||
|
|
})
|