push sheeet

pkgs/by-name/dr/dragmap/boost-iterator-range.patch

@@ -0,0 +1,12 @@
+diff --git a/src/lib/map/Mapper.cpp b/src/lib/map/Mapper.cpp
+index 6eaa2c5..781988c 100644
+--- a/src/lib/map/Mapper.cpp
++++ b/src/lib/map/Mapper.cpp
+@@ -22,6 +22,7 @@
+ //#include "common/Crc32Hw.hpp"
+ #include "common/DragenLogger.hpp"
+ #include "map/Mapper.hpp"
++#include <boost/range/iterator_range.hpp>
+ 
+ namespace dragenos {
+ namespace map {

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 {

pkgs/by-name/dr/dragmap/package.nix

@@ -0,0 +1,74 @@
+{
+  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 ];
+  };
+})

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;
+   }
+