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未找到 boost_thread，illumina bcl2fastq 1.8.3 安装错误，casava，illumina casava 也显示相同错误

tag-icon • tag-icon 14.04 cmake boost
未找到 boost_thread，illumina bcl2fastq 1.8.3 安装错误，casava，illumina casava 也显示相同错误

我正在尝试在 ubuntu 14.04 上安装 illumina bcl2fastq 1.8.3，cmake 是 2.8.4，boost 是 1.44。cmake 和 boost 都仅与 bcl2fastq 捆绑在一起。

我收到以下错误，有人可以解释一下这个错误吗，我看不懂。还请解释如何将 BOOST_LIBRARYDIR 设置为包含 Boost 库的目录或将 BOOST_ROOT 设置为 Boost 的位置。

CMake Error at /tmp/bcl2fastq_v1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:1128 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.44.0

  Boost include path: /tmp/bcl2fastq_v1.8.3-build/opt/bootstrap/include

  The following Boost libraries could not be found:

          boost_thread

  Some (but not all) of the required Boost libraries were found.  You may
  need to install these additional Boost libraries.  Alternatively, set
  BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
  to the location of Boost.
Call Stack (most recent call first):
  cmake/macros.cmake:93 (find_package)
  cmake/cxxConfigure.cmake:87 (casava_find_boost)
  c++/CMakeLists.txt:33 (include)


-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so 
-- using compiler: gcc version 4.9.1
-- Adding the c++    library subdirectory: common
-- Adding the c++    library subdirectory: io
-- Adding the c++    library subdirectory: alignment
-- Adding the c++    library subdirectory: basecalling
-- Adding the c++    library subdirectory: kagu
-- Adding the c++    library subdirectory: demultiplex
-- Adding the c++    program subdirectory: bin
-- Adding the c++    program subdirectory: BaseCalls
-- Adding the c++    program subdirectory: Demultiplex
-- Found Doxygen: /usr/bin/doxygen 
-- Doxygen: /usr/bin/doxygen. Dot: /usr/bin/dot.
-- Creating Doxygen config file: /tmp/bcl2fastq_v1.8.3-build/c++/Doxyfile
-- Configuring incomplete, errors occurred!
Couldn't configure the project:

/tmp/bcl2fastq_v1.8.3-build/bootstrap/bin/cmake -H"/tmp/BclToFastq/src" -B"/tmp/bcl2fastq_v1.8.3-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH= -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH= -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo

Moving CMakeCache.txt to CMakeCache.txt.removed

答案1

Bcl2Fastq 源代码无法在 Ubuntu 14.04 上编译。以下是在 14.04 上运行 RPM 二进制文件的替代说明（来源）：

sudo alien -i bcl2fastq-1.8.4-Linux-x86_64.rpm
sudo apt-get install build-essential
curl -kL http://install.perlbrew.pl | bash
echo >> ~/.bash_profile "source ~/perl5/perlbrew/etc/bashrc"
perlbrew install perl-5.14.4
perlbrew switch perl-5.14.4
perlbrew install-cpanm
cpanm XML/Simple.pm

笔记：

  • 以非 root 用户身份运行。
  • 在我的环境中，安装（构建）过程大约需要 10 分钟。
  • 您也可以使用“aptitude”代替“apt-get”。
  • 对于 perlbrew，您可以使用“use”而不是“switch”来仅为当前 shell 设置。您可能需要使用 cpanm 安装其他所需模块。

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