anaconda安装pysam报错

Question

anaconda 创建环境使用pip install pysam时出现出现以下报错：

Collecting pysam
  Using cached pysam-0.22.0.tar.gz (4.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [34 lines of output]
      # pysam: cython is available - using cythonize if necessary
      # pysam: htslib mode is shared
      # pysam: HTSLIB_CONFIGURE_OPTIONS=None
      '.' 不是内部或外部命令，也不是可运行的程序
      或批处理文件。
      '.' 不是内部或外部命令，也不是可运行的程序
      或批处理文件。
      # pysam: htslib configure options: None
      Traceback (most recent call last):
        File "D:\anaconda\envs\ivirp\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
          main()
        File "D:\anaconda\envs\ivirp\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "D:\anaconda\envs\ivirp\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
        File "C:\Users\Mr Xu\AppData\Local\Temp\pip-build-env-3i476mb_\overlay\Lib\site-packages\setuptools\build_meta.py", line 355, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "C:\Users\Mr Xu\AppData\Local\Temp\pip-build-env-3i476mb_\overlay\Lib\site-packages\setuptools\build_meta.py", line 325, in _get_build_requires
          self.run_setup()
        File "C:\Users\Mr Xu\AppData\Local\Temp\pip-build-env-3i476mb_\overlay\Lib\site-packages\setuptools\build_meta.py", line 507, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "C:\Users\Mr Xu\AppData\Local\Temp\pip-build-env-3i476mb_\overlay\Lib\site-packages\setuptools\build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 442, in <module>
        File "<string>", line 82, in run_make_print_config
        File "D:\anaconda\envs\ivirp\lib\subprocess.py", line 415, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "D:\anaconda\envs\ivirp\lib\subprocess.py", line 493, in run
          with Popen(*popenargs, **kwargs) as process:
        File "D:\anaconda\envs\ivirp\lib\subprocess.py", line 858, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "D:\anaconda\envs\ivirp\lib\subprocess.py", line 1327, in _execute_child
          hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
      FileNotFoundError: [WinError 2] 系统找不到指定的文件。
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

求解决方法

Answer 1

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---

这个错误是由于缺少某些必要的文件导致的。根据报错信息中的FileNotFoundError: [WinError 2] 系统找不到指定的文件，可能是因为某个文件无法找到。
解决方法可以尝试以下步骤：

1. 确保你的操作系统上已经安装了Cython。你可以尝试在命令行中运行以下命令来安装Cython：

   pip install cython
   

2. 安装HTSlib。HTSlib是Pysam的依赖库，如果其找不到，则会导致安装失败。你可以尝试在命令行中运行以下命令来安装HTSlib：

   conda install -c bioconda htslib
   

3. 如果以上步骤都没有解决问题，可以尝试删除Pysam的缓存文件，并重新安装：

   pip cache purge
   pip install pysam
   

如果问题仍然存在，请提供完整的错误日志以便能更好地帮助你解决问题。