MacOS下编译RSEM失败，运行提示rsem-parse-alignments不存在

问题详情 #

编译阶段错误 #

下载用于RNA-Seq基因/转录本表达量估算的RSEM软件包后，在MacOS终端进入软件目录执行make命令编译，出现大量boost库相关编译错误，核心错误片段如下：

In file included from simulation.cpp:22:
In file included from ./SingleModel.h:16:
In file included from ./Orientation.h:8:
In file included from ./simul.h:6:
In file included from ./boost/random.hpp:52:
In file included from ./boost/random/generate_canonical.hpp:22:
In file included from ./boost/math/special_functions.hpp:15:
In file included from ./boost/math/special_functions/airy.hpp:10:
In file included from ./boost/math/special_functions/bessel.hpp:21:
In file included from ./boost/math/special_functions/detail/bessel_jy_zero.hpp:25:
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:91:24: error: no template named 'tuple' in namespace 'boost::math'
          boost::math::tuple<T, T> operator()(const T& x) const
          ~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:94:33: error: no member named 'make_tuple' in namespace 'boost::math'
            return boost::math::make_tuple(
                   ~~~~~~~~~~~~~^
// 其余错误省略
fatal error: too many errors emitted, stopping now [-ferror-limit=]
6 warnings and 20 errors generated.
make: *** [simulation.o] Error 1

运行阶段错误 #

编译失败后尝试执行以下RSEM命令：

./rsem-calculate-expression --bowtie2 --bowtie2-path /Users/Documents/Bioinformatics_tools/Bowtie2/bowtie2-2.5.0-macos-x86_64  -p 8  --output-genome-bam --paired-end /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_1.fastq /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_2.fastq /Users/Documents/Bioinformatics_tools/Bowtie2/index/GRCh38_noalt_as/GRCh38_noalt_as  hg_paired_end_quals

收到错误提示：

rsem-parse-alignments : No such file or directory!

推测是编译未生成该可执行文件，已排查相关issue但未解决。

可行解决方案 #

• 优先使用预编译版本：直接下载官方提供的MacOS预编译RSEM包，解压后即可直接使用所有命令，彻底规避编译阶段的boost兼容问题。
• 修改boost头文件修复编译：若坚持源码编译，修改RSEM自带的两个boost头文件：
  1. 打开./boost/math/special_functions/detail/airy_ai_bi_zero.hpp和./boost/math/special_functions/detail/bessel_jy_zero.hpp
  2. 将文件中所有boost::math::tuple替换为std::tuple，boost::math::make_tuple替换为std::make_tuple
  3. 在每个文件开头添加#include <tuple>
  4. 执行make clean && make重新编译
• 指定低版本编译器：MacOS自带clang版本过高可能引发兼容问题，安装低版本llvm并指定编译：

  brew install llvm@11
  export CC=/usr/local/opt/llvm@11/bin/clang
  export CXX=/usr/local/opt/llvm@11/bin/clang++
  make clean && make
  

内容的提问来源于stack exchange，提问作者MOHAMMED TOUFIQ