From c35f615aea0cbfcbed0cc7c0fde1fc46f7d3edd3 Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis.praga@proton.me>
Date: Fri, 19 Apr 2024 15:10:26 +0200
Subject: [PATCH] dragmap: init at 1.3.0

Genomic mapper. Open-source version of DRAGEN.
Tests are run during execution with google-tests.
---
 pkgs/by-name/dr/dragmap/cstdint.patch      | 60 +++++++++++++++++++
 pkgs/by-name/dr/dragmap/package.nix        | 68 ++++++++++++++++++++++
 pkgs/by-name/dr/dragmap/stdio-pclose.patch | 12 ++++
 3 files changed, 140 insertions(+)
 create mode 100644 pkgs/by-name/dr/dragmap/cstdint.patch
 create mode 100644 pkgs/by-name/dr/dragmap/package.nix
 create mode 100644 pkgs/by-name/dr/dragmap/stdio-pclose.patch

diff --git a/pkgs/by-name/dr/dragmap/cstdint.patch b/pkgs/by-name/dr/dragmap/cstdint.patch
new file mode 100644
index 000000000000..b9b0721173d7
--- /dev/null
+++ b/pkgs/by-name/dr/dragmap/cstdint.patch
@@ -0,0 +1,60 @@
+diff --git a/src/include/map/SeedPosition.hpp b/src/include/map/SeedPosition.hpp
+index 30a7d47..c05af16 100644
+--- a/src/include/map/SeedPosition.hpp
++++ b/src/include/map/SeedPosition.hpp
+@@ -16,6 +16,7 @@
+ #define MAP_SEED_POSITION_HPP
+ 
+ #include <ostream>
++#include <cstdint>
+ 
+ #include "sequences/Seed.hpp"
+ 
+diff --git a/src/include/sequences/Read.hpp b/src/include/sequences/Read.hpp
+index 460c1cb..c7ff619 100644
+--- a/src/include/sequences/Read.hpp
++++ b/src/include/sequences/Read.hpp
+@@ -16,6 +16,7 @@
+ #define SEQUENCES_READ_HPP
+ 
+ #include <iostream>
++#include <cstdint>
+ #include <string>
+ #include <vector>
+ 
+diff --git a/src/include/sequences/Seed.hpp b/src/include/sequences/Seed.hpp
+index a242153..dd4d23b 100644
+--- a/src/include/sequences/Seed.hpp
++++ b/src/include/sequences/Seed.hpp
+@@ -16,6 +16,7 @@
+ #define SEQUENCES_SEED_HPP
+ 
+ #include <ostream>
++#include <cstdint>
+ #include <vector>
+ 
+ #include "sequences/Read.hpp"
+diff --git a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
+index 1866be7..5d9b7d7 100644
+--- a/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
++++ b/src/lib/sequences/tests/unit/CrcHasherMocks.hpp
+@@ -2,6 +2,7 @@
+ 
+ #include <array>
+ #include <cassert>
++#include <cstdint>
+ #include <cstdlib>
+ #include <string>
+ 
+diff --git a/stubs/dragen/src/host/dragen_api/read_group_list.hpp b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
+index eefb9ae..623a77f 100644
+--- a/stubs/dragen/src/host/dragen_api/read_group_list.hpp
++++ b/stubs/dragen/src/host/dragen_api/read_group_list.hpp
+@@ -14,6 +14,7 @@
+ #define __READ_GROUP_LIST_HPP__
+ 
+ #include "dragen_exception.hpp"
++#include <cstdint>
+ class ReadGroupList {
+ public:
+   const std::string &getReadGroupName(const uint16_t idx) const {
diff --git a/pkgs/by-name/dr/dragmap/package.nix b/pkgs/by-name/dr/dragmap/package.nix
new file mode 100644
index 000000000000..9f61cbb3e5e4
--- /dev/null
+++ b/pkgs/by-name/dr/dragmap/package.nix
@@ -0,0 +1,68 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  boost,
+  gtest,
+  zlib,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "dragmap";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "Illumina";
+    repo = "DRAGMAP";
+    rev = 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
+  ];
+
+  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 = with lib; {
+    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.
+    '';
+    license = licenses.gpl3;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ apraga ];
+  };
+})
diff --git a/pkgs/by-name/dr/dragmap/stdio-pclose.patch b/pkgs/by-name/dr/dragmap/stdio-pclose.patch
new file mode 100644
index 000000000000..74e8d57e9fa5
--- /dev/null
+++ b/pkgs/by-name/dr/dragmap/stdio-pclose.patch
@@ -0,0 +1,12 @@
+diff --git a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
+index cd02cd4..c26e9cf 100644
+--- a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
++++ b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
+@@ -57,7 +57,6 @@ int GetDmiValue(const std::string& label, std::string& value)
+   FILE* dmiOutput = popen("sudo /usr/sbin/dmidecode -t 2", "r");
+   if (dmiOutput == NULL) {
+     perror("dmidecode popen");
+-    pclose(dmiOutput);
+     return -1;
+   }
+