下载 Cygwin

从官网上下载：https://www.cygwin.com/

每一次安装编译新软件都需要点击 setup.exe，如下图所示

这一页选择从互联网下载动态库

选择下载的文件夹，一路点下一步

这里选择下载源，我选的是阿里云的

这个页面选择要下载的动态库，通常去待安装的源码种查看依赖库，并从这个页面下载，如果需要再次下载，则点击 Cygwin 的setup.exe来到这个页面，再次选择要下载的动态库
选择下载完毕后，点击下一步进行安装即可，安装库完毕以后，重启一下Cygwin

以编译fastANI为例

从https://github.com/ParBLiSS/FastANI下载源码，并且放入 Cygwin 的目录下（与bin同级），解压缩到当前目录，然后查看 INSTALL.txt 的安装说明

mkdir build 
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build .

如果在cmake的时候有缺少库报错，缺少哪一个则安装哪一个就可以，这里对CMakeLists.txt文件做了些许改动，

cmake_minimum_required(VERSION 3.20)
project(FastANI
    VERSION 1.34
    DESCRIPTION "Fast computation of whole-genome Average Nucleotide Identity (ANI)."
    LANGUAGES CXX)
#
# Main executable
add_executable(fastANI src/cgi/core_genome_identity.cpp src/cgi/main.cpp)
target_include_directories(fastANI PUBLIC "src/")
#
# by default, static linking
option(GSL_SHARED "Build using shared libraries" ON)
option(BUILD_TESTING "Build tests" ON) # build tests
#
# zlib dependency
find_package(ZLIB 1.1 REQUIRED)
if(${ZLIB_FOUND})
    message("Using zlib library v${ZLIB}")
endif(${ZLIB_FOUND})
target_link_libraries(fastANI PUBLIC ZLIB::ZLIB)
#
# openmp dependency
find_package(OpenMP)
if(${OpenMP_CXX_FOUND})
    message("Using OpenMP_CXX v${OpenMP_CXX_LIBRARIES}")
    message("Using OpenMP_CXX v${OpenMP_CXX_VERSION}")
    target_link_libraries(fastANI PUBLIC ${OpenMP_CXX_LIBRARIES})
    target_include_directories(fastANI PUBLIC ${OpenMP_CXX_INCLUDE_DIRS})
    target_compile_options(fastANI PUBLIC ${OpenMP_CXX_FLAGS})
else()
    message("NOTE: OpenMP not found; Compiling as a single threaded app...")
endif(${OpenMP_CXX_FOUND})
#
# GSL or Boost math
find_package(GSL 1.6)
if(${GSL_FOUND})
    message("GSL v${GSL_VERSION} Found: ${GSL_LIBDIR}")
    if(${GSL_SHARED})
        target_link_libraries(fastANI PUBLIC ${GSL_LIBRARIES})
    else()
        # GSL_LIBDIR is not documented
        target_link_libraries(fastANI PUBLIC
                ${GSL_LIBDIR}/libgsl.a
                ${GSL_LIBDIR}/libgslcblas.a)
    endif(${GSL_SHARED})

    target_include_directories(fastANI PUBLIC ${GSL_INCLUDE_DIRS})
else()
    set(Boost_USE_STATIC_LIBS        ON)  # only find static libs
    set(Boost_USE_DEBUG_LIBS        OFF)  # ignore debug libs and
    set(Boost_USE_RELEASE_LIBS       ON)  # only find release libs
    set(Boost_USE_MULTITHREADED      ON)
    find_package(Boost 1.45 REQUIRED COMPONENTS math_c99)
    target_link_libraries(fastANI PUBLIC ${Boost_MATCH_C99_LIBRARY})
    target_include_directories(fastANI PUBLIC ${Boost_INCLUDE_DIRS})
    target_compile_definitions(fastANI PUBLIC USE_BOOST=1)
endif(${GSL_FOUND})
#
#
if(${BUILD_TESTING})
    add_subdirectory(ext/Catch2)
    include(CTest)
    include(Catch)
    add_executable(fastANITest tests/fastani_tests.cpp src/cgi/core_genome_identity.cpp)
    target_include_directories(fastANITest PUBLIC "src/"
                            ${OpenMP_CXX_INCLUDE_DIRS})
    target_compile_options(fastANITest PUBLIC
            --coverage -g -O0 -fprofile-arcs -ftest-coverage ${OpenMP_CXX_FLAGS})
    target_link_libraries(fastANITest PRIVATE
                          Catch2::Catch2 Catch2::Catch2WithMain
                          GSL::gsl GSL::gslcblas
                          ${OpenMP_CXX_LIBRARIES}
                          gcov)

    # 改动部分
    target_link_libraries(fastANI PUBLIC ZLIB::ZLIB)
    catch_discover_tests(fastANITest)
    file(COPY tests/data DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
    add_custom_target(lcov lcov -c -d .. -o fastANITest.out
                        COMMAND genhtml -o ../lcov/ fastANITest.out
                        DEPENDS fastANITest)
    add_custom_target(lcov2 lcov -c -d ./ -o fastANITest.info
                        COMMAND lcov -e fastANITest.info "*/FastANI/src/*/*.cpp" "*/FastANI/src/*/*.hpp"  > coverage.info
                        COMMAND lcov --list coverage.info |tee coverage_list.txt
                        COMMAND lcov --summary coverage.info |tee coverage_summary.txt
                        DEPENDS fastANITest)
endif(${BUILD_TESTING})

install(TARGETS fastANI DESTINATION bin)

set(CPACK_GENERATOR "TGZ")
set(CPACK_SOURCE_GENERATOR "TGZ")
set(CPACK_PACKAGE_DIRECTORY ${PROJECT_BINARY_DIR}/package)

set(CPACK_SOURCE_IGNORE_FILES .git/ .github/ 
    .vscode/ .cache/ .mypy_cache/
    .idea/ complie_comands.json
    lcov/ lcov0/ lcov2/ data/ cmake-build-debug/
    _CPack_Packages/ build.sh/ build/  build.clang/
    ${CMAKE_BINARY_DIR}/ ${PROJECT_BINARY_DIR}/)

include(CPack)

打开 cygwin 终端，然后按照INSTALL.txt进行编译和安装：

mkdir build 
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release [--install-prefix ...  -DGSL_SHARED=... -DGSL_ROOT_DIR=... -DBOOST_ROOT=...]
cmake --build .

就可以在 build 文件夹下生成 fastANI.exe文件了