Import Module error Pysam
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2.1 years ago

I tried installing Pysam for using in Anaconda jupyter notebook and I get the following error:

 ERROR: Complete output from command python setup.py egg_info:
    ERROR: # 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.
    # pysam: htslib configure options: None
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "c:\users\prahalad\appdata\local\temp\pip-install-ikc6b_\pysam\setup.py", line 241, in <module>
        htslib_make_options = run_make_print_config()
      File "c:\users\prahalad\appdata\local\temp\pip-install-ikc6b_\pysam\setup.py", line 68, in run_make_print_config
        stdout = subprocess.check_output(["make", "-s", "print-config"])
      File "C:\ProgramData\Anaconda2\lib\subprocess.py", line 216, in check_output
        process = Popen(stdout=PIPE, *popenargs, **kwargs)
      File "C:\ProgramData\Anaconda2\lib\subprocess.py", line 394, in __init__
        errread, errwrite)
      File "C:\ProgramData\Anaconda2\lib\subprocess.py", line 644, in _execute_child
        startupinfo)
    WindowsError: [Error 2] The system cannot find the file specified
    ----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in c:\users\prahalad\appdata\local\temp\pip-install-ikc6b_\pysam\
snp pysam • 1.7k views
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You might mention that you're using windows, since very few packages actively support it.

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