dragmap: drop

Failing Hydra build: https://hydra.nixos.org/build/344145730 Repo is archived as well.
2026-09-29 03:10:19 +00:00 · 2026-09-03 18:21:11 +02:00
parent ac80cd0e95
commit 829921e643
6 changed files with 1 additions and 190 deletions
--- a/pkgs/by-name/dr/dragmap/boost-iterator-range.patch
+++ b/pkgs/by-name/dr/dragmap/boost-iterator-range.patch
@@ -1,12 +0,0 @@
-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 {
--- a/pkgs/by-name/dr/dragmap/cstdint.patch
+++ b/pkgs/by-name/dr/dragmap/cstdint.patch
@@ -1,73 +0,0 @@
-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/stubs/dragen/src/host/metrics/public/run_stats.hpp b/stubs/dragen/src/host/metrics/public/run_stats.hpp
-index 998fe4e..9561b0b 100644
--- a/stubs/dragen/src/host/metrics/public/run_stats.hpp
-+++ b/stubs/dragen/src/host/metrics/public/run_stats.hpp
-@@ -10,6 +10,7 @@
- #include <string>
- #include <vector>
- #include <memory>
-+#include <cstdint>
- //
- // RP: HA! HA! HA! That's what you get when you write code logging to cout all
- // over the place!
--- a/pkgs/by-name/dr/dragmap/getHostVersion.patch
+++ b/pkgs/by-name/dr/dragmap/getHostVersion.patch
@@ -1,11 +0,0 @@
-diff --git a/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c b/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c
-index cdca3df..5a55699 100644
--- a/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c
-+++ b/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c
-@@ -249,7 +249,7 @@ void setDefaultHashParams(hashTableConfig_t* defConfig, const char* destDir, Has
-     free(dir);
-   }
-
-  defConfig->hostVersion = (char*)getHostVersion(0);
-+  defConfig->hostVersion = (char*)getHostVersion();
- }
--- a/pkgs/by-name/dr/dragmap/package.nix
+++ b/pkgs/by-name/dr/dragmap/package.nix
@@ -1,82 +0,0 @@
-{
-  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
-  ];
-
-  # Latest boost do not need system as a linking flag
-  postPatch = ''
-    sed -i 's/system filesystem/filesystem/' config.mk
-  '';
-
-  patches = [
-    # getHostVersion use an empty parameter list. This is now an error for GC
-    ./getHostVersion.patch
-
-    # 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 $out/bin/
-
-    runHook postInstall
-  '';
-
-  # Tests are launched by default from makefile
-  doCheck = false;
-
-  meta = {
-    description = "Open Source version of Dragen mapper for genomics";
-    mainProgram = "dragen-os";
-    longDescription = ''
-      DRAGMAP is an open-source software implementation of the DRAGEN mapper,
-      which the Illumina team created to produce the same results as their
-      proprietary DRAGEN hardware.
-    '';
-    homepage = "https://github.com/Illumina/DRAGMAP";
-    changelog = "https://github.com/Illumina/DRAGMAP/releases/tag/${finalAttrs.version}";
-    license = lib.licenses.gpl3;
-    platforms = [ "x86_64-linux" ];
-    maintainers = with lib.maintainers; [ apraga ];
-  };
-})
--- a/pkgs/by-name/dr/dragmap/stdio-pclose.patch
+++ b/pkgs/by-name/dr/dragmap/stdio-pclose.patch
@@ -1,12 +0,0 @@
-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;
-   }
- 
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -722,6 +722,7 @@ mapAliases {
  dotnetfx40 = throw "'dotnetfx40' has been removed because it was unmaintained in Nixpkgs"; # Added 2026-01-27
  dotty = throw "'dotty' has been renamed to/replaced by 'scala_3'"; # Converted to throw 2025-10-27
  dovecot_fts_xapian = throw "'dovecot_fts_xapian' has been removed because it was unmaintained in Nixpkgs. Consider using dovecot-fts-flatcurve instead"; # Added 2025-08-16
+  dragmap = throw "'dragmap' doesn't build with latest glibc anymore and upstream repo is archived"; # Added 2026-09-03
  drone-runner-exec = throw "'drone-runner-exec' has been removed as it was deprecated and archived upstream."; # Added 2026-07-20
  dsd = throw "dsd has been removed, as it was broken and lack of upstream maintenance"; # Added 2025-08-25
  dtv-scan-tables_linuxtv = throw "'dtv-scan-tables_linuxtv' has been renamed to/replaced by 'dtv-scan-tables'"; # Converted to throw 2025-10-27