为什么安装pysam python包会失败？

Question

我不熟悉python并运行命令：

pip安装pysam

其结果是：

Collecting pysam
  Using cached https://files.pythonhosted.org/packages/25/7e/098753acbdac54ace0c6dc1f8a74b54c8028ab73fb027f6a4215487d1fea/pysam-0.15.4.tar.gz
    ERROR: Command errored out with exit status 1:
     command: 'c:\path\programs\python\python38\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\path\\Local\\Temp\\pip-install-qzuue1yz\\pysam\\setup.py'"'"'; __file__='"'"'C:\\path\\Temp\\pip-install-qzuue1yz\\pysam\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
    Complete output (23 lines):
    # pysam: cython is available - using cythonize if necessary
    # pysam: htslib mode is shared
    # pysam: HTSLIB_CONFIGURE_OPTIONS=None
    '.' is not recognized as an internal or external command,
    operable program or batch file.
    '.' is not recognized as an internal or external command,
    operable program or batch file.
      File "<string>", line 1, in <module>
      File "C:\path\Local\Temp\pip-install-qzuue1yz\pysam\setup.py", line 241, in <module>
        htslib_make_options = run_make_print_config()
      File "C:\path\\Local\Temp\pip-install-qzuue1yz\pysam\setup.py", line 68, in run_make_print_config
        stdout = subprocess.check_output(["make", "-s", "print-config"])
      File "c:\path\programs\python\python38\lib\subprocess.py", line 411, in check_output
        return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
      File "c:\path\programs\python\python38\lib\subprocess.py", line 489, in run
      File "c:\path\programs\python\python38\lib\subprocess.py", line 854, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "c:\path\programs\python\python38\lib\subprocess.py", line 1307, in _execute_child
        hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
    FileNotFoundError: [WinError 2] The system cannot find the file specified
    # pysam: htslib configure options: None
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

这里有什么问题？

最初，我遇到了一个关于cython没有安装的错误，所以我运行，这样就可以在没有问题的情况下运行它。

Answer 1

有许多二进制车轮在PyPI，但只适用于Linux和MacOS X。生物康达的包裹也只为Linux和OS编译。

当您尝试在Windows pip上安装pysam时，下载源代码发行版pysam-0.15.4.tar.gz，解压缩它并运行setup.y

pysam的setup.py 配置库htslib由正在运行脚本htslib/configure编写。这是一个shell脚本，如果没有Unix仿真层，它就不能在Windows中运行。因此出现了错误。

一句话:和许多与遗传学相关的软件一样(我对用Python和Java编写的软件有一些经验)，pysam似乎只适用于Unix，最好是Linux或OS。

Answer 2

如果你有蟒蛇，试试这个：

conda install -c bioconda pysam