pyrox.dev
dragmap: init at 1.3.0
Genomic mapper. Open-source version of DRAGEN.
Tests are run during execution with google-tests.
authored by Alexis Praga and committed by Alexis Praga c35f615a da5c2592
+60
pkgs/by-name/dr/dragmap/cstdint.patch
+60
pkgs/by-name/dr/dragmap/cstdint.patch
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diff --git a/src/include/map/SeedPosition.hpp b/src/include/map/SeedPosition.hpp
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index 30a7d47..c05af16 100644
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--- a/src/include/map/SeedPosition.hpp
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+++ b/src/include/map/SeedPosition.hpp
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@@ -16,6 +16,7 @@
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#define MAP_SEED_POSITION_HPP
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#include <ostream>
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+#include <cstdint>
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#include "sequences/Seed.hpp"
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diff --git a/src/include/sequences/Read.hpp b/src/include/sequences/Read.hpp
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index 460c1cb..c7ff619 100644
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--- a/src/include/sequences/Read.hpp
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+++ b/src/include/sequences/Read.hpp
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@@ -16,6 +16,7 @@
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#define SEQUENCES_READ_HPP
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#include <iostream>
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+#include <cstdint>
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#include <string>
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#include <vector>
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diff --git a/src/include/sequences/Seed.hpp b/src/include/sequences/Seed.hpp
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index a242153..dd4d23b 100644
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--- a/src/include/sequences/Seed.hpp
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+++ b/src/include/sequences/Seed.hpp
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@@ -16,6 +16,7 @@
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#define SEQUENCES_SEED_HPP
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#include <ostream>
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+#include <cstdint>
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#include <vector>
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#include "sequences/Read.hpp"
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diff --git a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
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index 1866be7..5d9b7d7 100644
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--- a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
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+++ b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
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@@ -2,6 +2,7 @@
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+
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#include <array>
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#include <cassert>
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+#include <cstdint>
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#include <cstdlib>
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#include <string>
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diff --git a/stubs/dragen/src/host/dragen_api/read_group_list.hpp b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
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index eefb9ae..623a77f 100644
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--- a/stubs/dragen/src/host/dragen_api/read_group_list.hpp
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+++ b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
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@@ -14,6 +14,7 @@
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#define __READ_GROUP_LIST_HPP__
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+
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#include "dragen_exception.hpp"
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+#include <cstdint>
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class ReadGroupList {
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public:
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const std::string &getReadGroupName(const uint16_t idx) const {
+68
pkgs/by-name/dr/dragmap/package.nix
+68
pkgs/by-name/dr/dragmap/package.nix
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{
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lib,
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stdenv,
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fetchFromGitHub,
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boost,
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gtest,
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zlib,
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "dragmap";
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version = "1.3.0";
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src = fetchFromGitHub {
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owner = "Illumina";
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repo = "DRAGMAP";
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rev = finalAttrs.version;
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fetchSubmodules = true;
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hash = "sha256-f1jsOErriS1I/iUS4CzJ3+Dz8SMUve/ccb3KaE+L7U8=";
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};
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nativebuildInputs = [ boost ];
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buildInputs = [
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gtest
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zlib
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];
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patches = [
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# pclose is called on a NULL value. This is no longer allowed since
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# https://github.com/bminor/glibc/commit/64b1a44183a3094672ed304532bedb9acc707554
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./stdio-pclose.patch
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# Add missing include cstdint. Upstream does not accept PR. Issue opened at
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# https://github.com/Illumina/DRAGMAP/issues/63
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./cstdint.patch
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];
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env = {
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GTEST_INCLUDEDIR = "${gtest.dev}/include";
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CPPFLAGS = "-I ${boost.dev}/include";
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LDFLAGS = "-L ${boost.out}/lib";
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};
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin
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cp build/release/dragen-os $out/bin/
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runHook postInstall
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'';
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# Tests are launched by default from makefile
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doCheck = false;
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meta = with lib; {
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description = "Open Source version of Dragen mapper for genomics";
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mainProgram = "dragen-os";
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longDescription = ''
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DRAGMAP is an open-source software implementation of the DRAGEN mapper,
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which the Illumina team created to procude the same results as their
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proprietary DRAGEN hardware.
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'';
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license = licenses.gpl3;
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platforms = platforms.unix;
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maintainers = with maintainers; [ apraga ];
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};
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})
+12
pkgs/by-name/dr/dragmap/stdio-pclose.patch
+12
pkgs/by-name/dr/dragmap/stdio-pclose.patch
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diff --git a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
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index cd02cd4..c26e9cf 100644
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--- a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
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+++ b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
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@@ -57,7 +57,6 @@ int GetDmiValue(const std::string& label, std::string& value)
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FILE* dmiOutput = popen("sudo /usr/sbin/dmidecode -t 2", "r");
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if (dmiOutput == NULL) {
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perror("dmidecode popen");
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- pclose(dmiOutput);
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return -1;
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}
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