easybuilders · pavelToman · Mar 27, 2026 · Mar 27, 2026 · Mar 30, 2026
diff --git a/easybuild/easyconfigs/d/dorado/dorado-1.4.0-foss-2025a-CUDA-12.8.0.eb b/easybuild/easyconfigs/d/dorado/dorado-1.4.0-foss-2025a-CUDA-12.8.0.eb
@@ -0,0 +1,84 @@
+easyblock = 'CMakeMake'
+
+name = 'dorado'
+version = '1.4.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/dorado'
+description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
+
+toolchain = {'name': 'foss', 'version': '2025a'}
+toolchainopts = {'usempi': False}
+
+source_urls = ['https://github.com/nanoporetech/dorado/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/nanoporetech',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_XZ,
+}]
+patches = [
+    'dorado-1.4.0_fix-hts-cmake.patch',
+    'dorado-1.4.0_fix-TestUtils.h.patch',
+]
+checksums = [
+    {'dorado-1.4.0.tar.xz': 'b65aaaeacd9169ecf3722b4e37956f74ae4ac9ce09827d3bb4cdef1ec82e6965'},
+    {'dorado-1.4.0_fix-hts-cmake.patch': 'b99f268086650462437cc252040bb8636dfe1e1bbb566e65590fd3401d63f2a0'},
+    {'dorado-1.4.0_fix-TestUtils.h.patch': 'f99f0de9506ad9e58be508ae353546e94eb77c6ae5b085637060ec83331ad5ed'},
+]
+
+builddependencies = [
+    ('CMake', '3.31.3'),
+    ('git', '2.49.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.8.0', '', SYSTEM),
+    ('Python', '3.13.1'),
+    ('OpenSSL', '3', '', SYSTEM),
+    ('PyTorch', '2.9.1', versionsuffix),
+    ('HDF5', '1.14.6'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.22.1'),
+    ('kineto', '20260317', versionsuffix),
+    ('libaec', '1.1.4'),
+]
+
+# don't link to OpenSSL static libraries
+# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
+preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
+# replace dont_install_external_libraries.patch by sed cmd - use system CUDA
+preconfigopts += "sed -i '/install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)/d' "
+preconfigopts += "../dorado/cmake/InstallRedistLibs.cmake && "
+# disable treating warnings like errors by stripping out -Werror
+# cfr. https://github.com/nanoporetech/dorado/issues/779
+preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+
+local_torch_root_py = 'import torch, pathlib; print(pathlib.Path(torch.__file__).resolve().parent)'
+configopts = ' '.join([
+    "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
+    "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc",
+    '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL',
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_CXX_FLAGS="$CXXFLAGS -pthread"',
+    # let torch find its files - different paths for PyTorch from sources and wheels
+    rf'''-DDORADO_LIBTORCH_DIR="$(python -s -c '{local_torch_root_py}')"''',
+    r'''-DCMAKE_PREFIX_PATH="$(python -s -c 'import torch; print(torch.utils.cmake_prefix_path)')"''',
+]) + ' '
+
+runtest = True
+
+sanity_check_paths = {
+    'files': ['bin/dorado'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["dorado basecaller --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-TestUtils.h.patch b/easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-TestUtils.h.patch
@@ -0,0 +1,23 @@
+Replace std::filesystem::remove_all with rm -rf in test temp-dir cleanup to avoid
+segfault with PyTorch 2.9.1-loaded filesystem symbols
+Author: Pavel Tomanek (Inuits/Ugent) with help of ChatGPT5.4
+--- tests/TestUtils.h.orig	2026-03-27 16:30:29.957036727 +0100
++++ tests/TestUtils.h	2026-03-27 16:31:17.700602831 +0100
+@@ -2,6 +2,7 @@
+
+ #include <spdlog/spdlog.h>
+
++#include <cstdlib>
+ #include <cstring>
+ #include <filesystem>
+ #include <string>
+@@ -44,7 +45,8 @@
+             while (!deleted && tries < 5) {
+                 try {
+                     tries++;
+-                    deleted = std::filesystem::remove_all(m_path);
++                    std::string cmd = "rm -rf -- \"" + m_path.string() + "\"";
++                    deleted = (std::system(cmd.c_str()) == 0) ? 1 : 0;
+                 } catch (std::exception& e) {
+                     std::string what = e.what();
+                     spdlog::warn(what);
diff --git a/easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-hts-cmake.patch b/easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-hts-cmake.patch
@@ -0,0 +1,118 @@
+Replace vendored HTSlib CMake integration with system HTSlib target
+Author: Pavel Tomanek (Inuits/Ugent) with help of ChatGPT5.4
+--- cmake/Htslib.cmake.orig	2026-03-27 16:02:28.928335000 +0100
++++ cmake/Htslib.cmake	2026-03-27 16:03:27.115524695 +0100
+@@ -1,100 +1,14 @@
+-if(NOT TARGET htslib) # lazy include guard
+-    if(WIN32)
+-        message(STATUS "Fetching htslib")
+-        download_and_extract(
+-            ${DORADO_CDN_URL}/htslib-win-v1.22.1.tar.gz
+-            htslib-win
+-            "8cedc027d0c796e6fe6c8e30fe8ec161c46122d9ab66d5d6339f039ffc91b2ea"
+-        )
+-        set(HTSLIB_DIR ${DORADO_3RD_PARTY_DOWNLOAD}/htslib-win CACHE STRING
+-                    "Path to htslib repo")
+-        add_library(htslib SHARED IMPORTED)
+-        set_target_properties(htslib PROPERTIES 
+-            "IMPORTED_IMPLIB" ${HTSLIB_DIR}/hts-3.lib
+-            "IMPORTED_LOCATION" ${HTSLIB_DIR}/hts-3.dll
+-            "INTERFACE_INCLUDE_DIRECTORIES" ${HTSLIB_DIR})
+-        target_link_directories(htslib INTERFACE ${HTSLIB_DIR})
+-    else()
+-        message(STATUS "Setting up htslib build")
+-        set(HTSLIB_DIR ${DORADO_3RD_PARTY_SOURCE}/htslib CACHE STRING "Path to htslib repo")
+-        set(htslib_PREFIX ${CMAKE_BINARY_DIR}/3rdparty/htslib)
+-
+-        find_program(MAKE_COMMAND make REQUIRED)
+-        find_program(AUTOCONF_COMMAND autoconf REQUIRED)
+-        find_program(AUTOHEADER_COMMAND autoheader REQUIRED)
+-        execute_process(
+-            COMMAND bash -c "${AUTOCONF_COMMAND} -V | sed 's/.* //; q'"
+-            OUTPUT_VARIABLE AUTOCONF_VERS
+-            COMMAND_ERROR_IS_FATAL ANY
+-        )
+-        if (AUTOCONF_VERS VERSION_GREATER_EQUAL 2.70 AND NOT CMAKE_GENERATOR STREQUAL "Xcode")
+-            set(AUTOCONF_COMMAND autoreconf --install)
+-        endif()
+-
+-        # htslib will only try to build the .so as PIC, but ont_core needs it all as PIC.
+-        unset(hts_cflags)
+-        if (LINUX)
+-            set(hts_cflags "-fPIC")
+-        endif()
+-
+-        # If we're building with sanitizers then we need to build htslib the same way.
+-        if (ECM_ENABLE_SANITIZERS MATCHES "address")
+-            set(hts_cflags "${hts_cflags} -g -fsanitize=address")
+-        endif()
+-        if (ECM_ENABLE_SANITIZERS MATCHES "undefined")
+-            set(hts_cflags "${hts_cflags} -g -fsanitize=undefined")
+-        endif()
+-        if (ECM_ENABLE_SANITIZERS MATCHES "thread")
+-            set(hts_cflags "${hts_cflags} -g -fsanitize=thread")
+-        endif()
+-
+-        unset(hts_configure_flags)
+-        if (hts_cflags)
+-            set(hts_configure_flags "CPPFLAGS=${hts_cflags}" "LDFLAGS=${hts_cflags}")
+-        endif()
+-
+-        # Parallelise the htslib build too, though not enough to compete with the main build.
+-        include(ProcessorCount)
+-        ProcessorCount(nproc)
+-        math(EXPR htslib_build_jobs "${nproc} / 4")
+-        if (htslib_build_jobs EQUAL 0)
+-            set(htslib_build_jobs 1)
+-        endif()
+-
+-        # The Htslib build apparently requires BUILD_IN_SOURCE=1, which is a problem when
+-        # switching between build targets because htscodecs object files aren't regenerated.
+-        # To avoid this, copy the source tree to a build-specific directory and do the build there.
+-        set(HTSLIB_BUILD ${CMAKE_BINARY_DIR}/htslib_build)
+-        file(COPY ${HTSLIB_DIR} DESTINATION ${HTSLIB_BUILD})
+-
+-        include(ExternalProject)
+-        ExternalProject_Add(htslib_project
+-            PREFIX ${HTSLIB_BUILD}
+-            SOURCE_DIR ${HTSLIB_BUILD}/htslib
+-            BUILD_IN_SOURCE 1
+-            CONFIGURE_COMMAND ${AUTOHEADER_COMMAND}
+-            COMMAND ${AUTOCONF_COMMAND}
+-            COMMAND ./configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs --without-libdeflate ${hts_configure_flags}
+-            BUILD_COMMAND ${MAKE_COMMAND} -j${htslib_build_jobs} install prefix=${htslib_PREFIX}
+-            COMMAND ${INSTALL_NAME}
+-            INSTALL_COMMAND ""
+-            BUILD_BYPRODUCTS ${htslib_PREFIX}/lib/libhts.a
+-            LOG_CONFIGURE 0
+-            LOG_BUILD 0
+-            LOG_TEST 0
+-            LOG_INSTALL 0
+-        )
+-
+-        add_library(htslib STATIC IMPORTED)
+-        # Need to ensure this directory exists before we can add it to INTERFACE_INCLUDE_DIRECTORIES
+-        file(MAKE_DIRECTORY ${htslib_PREFIX}/include)
+-        set_target_properties(htslib 
+-            PROPERTIES 
+-                "IMPORTED_LOCATION" ${htslib_PREFIX}/lib/libhts.a
+-                "INTERFACE_INCLUDE_DIRECTORIES" ${htslib_PREFIX}/include)
+-        message(STATUS "Done configuring htslib")
+-
+-        # Make sure that the project is built before any targets try to use it.
+-        add_dependencies(htslib htslib_project)
+-    endif()
++if(NOT TARGET htslib)
++  find_package(htslib QUIET NO_MODULE)
++  if(htslib_FOUND AND TARGET htslib::hts)
++    add_library(htslib INTERFACE IMPORTED)
++    target_link_libraries(htslib INTERFACE htslib::hts)
++    message(STATUS "Using system htslib via config package")
++  else()
++    find_package(PkgConfig REQUIRED)
++    pkg_check_modules(HTSLIB REQUIRED IMPORTED_TARGET htslib)
++    add_library(htslib INTERFACE IMPORTED)
++    target_link_libraries(htslib INTERFACE PkgConfig::HTSLIB)
++    message(STATUS "Using system htslib via pkg-config")
++  endif()
+ endif()
diff --git a/easybuild/easyconfigs/k/kineto/kineto-20260317-GCC-14.2.0-CUDA-12.8.0.eb b/easybuild/easyconfigs/k/kineto/kineto-20260317-GCC-14.2.0-CUDA-12.8.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'kineto'
+version = '20260317'
+local_commit = '7d860f2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/pytorch/kineto'
+description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters"
+
+toolchain = {'name': 'GCC', 'version': '14.2.0'}
+
+source_urls = ['https://github.com/pytorch/kineto/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/pytorch',
+        'repo_name': name,
+        'commit': local_commit,
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_XZ,
+}]
+checksums = ['015ad66abc07c4120be0789168d34f5537dc8b87b0ad96775a3ba70a18894c96']
+
+builddependencies = [
+    ('CMake', '3.31.3'),
+    ('Python', '3.13.1'),
+]
+dependencies = [('CUDA', '12.8.0', '', SYSTEM)]
+
+start_dir = 'libkineto'
+
+sanity_check_paths = {
+    'files': ['lib/libkineto.a'],
+    'dirs': ['include/kineto'],
+}
+
+moduleclass = 'perf'