dorado: switching to source build (#42039)
* dorado: switching to source build * dorado: fixing formatting issue
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snehring
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var/spack/repos/builtin/packages/dorado/cmake-htslib.patch
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111
var/spack/repos/builtin/packages/dorado/cmake-htslib.patch
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@ -0,0 +1,111 @@
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diff --git a/CMakeLists.txt b/CMakeLists.txt
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index 64d6091e..323412a4 100755
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--- a/CMakeLists.txt
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+++ b/CMakeLists.txt
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@@ -316,10 +316,6 @@ target_link_libraries(dorado_lib
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minimap2
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)
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-if(NOT WIN32)
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- add_dependencies(dorado_lib htslib_project)
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-endif()
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-
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if(NOT DORADO_DISABLE_DORADO)
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if(NOT WIN32)
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# Set up RPATHs so we can find dependencies
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diff --git a/cmake/Htslib.cmake b/cmake/Htslib.cmake
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index caabc1a3..c72fe534 100644
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--- a/cmake/Htslib.cmake
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+++ b/cmake/Htslib.cmake
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@@ -1,68 +1,4 @@
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-if(NOT TARGET htslib) # lazy include guard
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- if(WIN32)
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- message(STATUS "Fetching htslib")
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- download_and_extract(https://cdn.oxfordnanoportal.com/software/analysis/htslib-win.tar.gz htslib-win)
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- set(HTSLIB_DIR ${DORADO_3RD_PARTY_DOWNLOAD}/htslib-win CACHE STRING
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- "Path to htslib repo")
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- add_library(htslib SHARED IMPORTED)
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- set_target_properties(htslib PROPERTIES
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- "IMPORTED_IMPLIB" ${HTSLIB_DIR}/hts-3.lib
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- "IMPORTED_LOCATION" ${HTSLIB_DIR}/hts-3.dll
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- "INTERFACE_INCLUDE_DIRECTORIES" ${HTSLIB_DIR})
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- target_link_directories(htslib INTERFACE ${HTSLIB_DIR})
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- else()
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- message(STATUS "Setting up htslib build")
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- set(HTSLIB_DIR ${DORADO_3RD_PARTY_SOURCE}/htslib CACHE STRING "Path to htslib repo")
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- set(htslib_PREFIX ${CMAKE_BINARY_DIR}/3rdparty/htslib)
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+include_directories(${HTSLIB_PREFIX}/include)
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- find_program(MAKE_COMMAND make REQUIRED)
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- find_program(AUTOCONF_COMMAND autoconf REQUIRED)
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- find_program(AUTOHEADER_COMMAND autoheader REQUIRED)
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- execute_process(COMMAND bash -c "${AUTOCONF_COMMAND} -V | sed 's/.* //; q'"
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- OUTPUT_VARIABLE AUTOCONF_VERS)
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- if (AUTOCONF_VERS VERSION_GREATER_EQUAL 2.70 AND NOT CMAKE_GENERATOR STREQUAL "Xcode")
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- set(AUTOCONF_COMMAND autoreconf --install)
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- endif()
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-
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- # The Htslib build apparently requires BUILD_IN_SOURCE=1, which is a problem when
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- # switching between build targets because htscodecs object files aren't regenerated.
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- # To avoid this, copy the source tree to a build-specific directory and do the build there.
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- set(HTSLIB_BUILD ${CMAKE_BINARY_DIR}/htslib_build)
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- file(COPY ${HTSLIB_DIR} DESTINATION ${HTSLIB_BUILD})
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-
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- if (CMAKE_SYSTEM_NAME STREQUAL "iOS")
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- # We need cross-compilation mode for iOS builds. Otherwise we end up trying to link a MacOS library
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- # into an iOS target.
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- set(CONFIGURE_FLAGS --host=aarch64-apple-darwin "CFLAGS=-isysroot ${CMAKE_OSX_SYSROOT}" "CC=${CMAKE_C_COMPILER}" "LDFLAGS=-isysroot ${CMAKE_OSX_SYSROOT}")
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- # By default the dylib install name will be some local path that won't work on the device.
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- set(INSTALL_NAME ${CMAKE_INSTALL_NAME_TOOL} -id "@executable_path/Frameworks/libhts.3.dylib" ${htslib_PREFIX}/lib/libhts.3.dylib)
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- endif()
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-
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- include(ExternalProject)
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- ExternalProject_Add(htslib_project
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- PREFIX ${HTSLIB_BUILD}
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- SOURCE_DIR ${HTSLIB_BUILD}/htslib
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- BUILD_IN_SOURCE 1
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- CONFIGURE_COMMAND ${AUTOHEADER_COMMAND}
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- COMMAND ${AUTOCONF_COMMAND}
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- COMMAND ./configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs ${CONFIGURE_FLAGS}
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- BUILD_COMMAND ${MAKE_COMMAND} install prefix=${htslib_PREFIX}
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- COMMAND ${INSTALL_NAME}
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- INSTALL_COMMAND ""
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- BUILD_BYPRODUCTS ${htslib_PREFIX}/lib/libhts.a
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- LOG_CONFIGURE 0
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- LOG_BUILD 0
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- LOG_TEST 0
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- LOG_INSTALL 0
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- )
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-
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- add_library(htslib STATIC IMPORTED)
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- # Need to ensure this directory exists before we can add it to INTERFACE_INCLUDE_DIRECTORIES
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- file(MAKE_DIRECTORY ${htslib_PREFIX}/include)
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- set_target_properties(htslib
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- PROPERTIES
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- "IMPORTED_LOCATION" ${htslib_PREFIX}/lib/libhts.a
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- "INTERFACE_INCLUDE_DIRECTORIES" ${htslib_PREFIX}/include)
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- message(STATUS "Done Building htslib")
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- endif()
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-endif()
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+add_library(htslib SHARED IMPORTED)
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+set_target_properties(htslib PROPERTIES IMPORTED_LOCATION ${HTSLIB_PREFIX}/lib/libhts.so)
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diff --git a/dorado/utils/CMakeLists.txt b/dorado/utils/CMakeLists.txt
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index 9bbf7067..e78feabe 100644
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--- a/dorado/utils/CMakeLists.txt
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+++ b/dorado/utils/CMakeLists.txt
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@@ -117,13 +117,9 @@ if(APPLE AND NOT CMAKE_SYSTEM_NAME STREQUAL "iOS")
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target_link_libraries(dorado_utils PUBLIC ${IOKIT})
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endif()
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-if(NOT WIN32)
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- add_dependencies(dorado_utils htslib_project)
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-endif()
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-
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# GCC 8 ICEs trying to compile this file with ASAN+optimisations enabled, so knock down the optimisation to try and help it out.
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if (ECM_ENABLE_SANITIZERS AND (CMAKE_CXX_COMPILER_ID MATCHES "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0))
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set_source_files_properties(duplex_utils.cpp PROPERTIES COMPILE_OPTIONS "-O0")
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endif()
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-enable_warnings_as_errors(dorado_utils)
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\ No newline at end of file
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+enable_warnings_as_errors(dorado_utils)
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@ -6,18 +6,37 @@
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from spack.package import *
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class Dorado(Package):
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"""
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Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
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"""
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class Dorado(CMakePackage, CudaPackage):
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"""Dorado is a high-performance, easy-to-use, open source basecaller
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for Oxford Nanopore reads."""
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homepage = "https://github.com/nanoporetech/dorado"
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url = "https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.5.1-linux-x64.tar.gz"
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git = "https://github.com/nanoporetech/dorado.git"
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url = "https://github.com/nanoporetech/dorado/archive/refs/tags/v0.5.1.tar.gz"
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version("0.5.1", sha256="7d95f4d47e0024db8ca275a5c591ebcaf2e17bfbff714fa824b212fb58a98802")
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maintainers("snehring")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install("bin/dorado", prefix.bin)
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mkdirp(prefix.lib)
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install_tree("lib/.", prefix.lib)
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version("0.5.1", commit="a7fb3e3d4afa7a11cb52422e7eecb1a2cdb7860f", submodules=True)
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depends_on("autoconf", type="build")
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depends_on("automake", type="build")
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depends_on("git", type="build")
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depends_on("curl", type="build")
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depends_on("cuda")
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depends_on("hdf5@1.17:+hl+cxx+szip")
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depends_on("htslib@1.15.1")
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depends_on("openssl")
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depends_on("zstd")
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depends_on("libdeflate")
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depends_on("zlib-api")
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patch("cmake-htslib.patch")
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def setup_build_environment(self, env):
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env.prepend_path("LD_LIBRARY_PATH", self.spec["libdeflate"].prefix.lib64)
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env.prepend_path("LIBRARY_PATH", self.spec["libdeflate"].prefix.lib64)
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def cmake_args(self):
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htslib_prefix = self.spec["htslib"].prefix
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args = [f"-DHTSLIB_PREFIX={htslib_prefix}", f"-DDORADO_INSTALL_PATH={self.prefix}"]
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return args
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