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wdecoster / nanopack

An overview of all nanopack tools
http://nanoplot.bioinf.be
GNU General Public License v3.0
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Command "python setup.py egg_info" failed with error code 1 in ... pysam #7

Closed KidneyPunch closed 5 years ago

KidneyPunch commented 5 years ago

Using Anaconda and pip install nanopack the process collects all the packages, then I get the following error:

(not showing previously fetched packages to save space, but they all fetched similar to NanoGUI)

Collecting NanoGUI (from nanopack)
  Using cached https://files.pythonhosted.org/packages/bd/a1/6cf74f2086e4e7215c740c28671337f01d126e9d2f4ec6ebacc47fd792de/NanoGUI-0.1.0.tar.gz
Requirement already satisfied: biopython in c:\programdata\anaconda3\lib\site-packages (from NanoPlot>=0.20.1->nanopack) (1.72)
Collecting pysam>0.10.0.0 (from NanoPlot>=0.20.1->nanopack)
  Using cached https://files.pythonhosted.org/packages/73/59/c319f1bde3019bbce4583cecb12b9e3e52ffcfbe2c96d8b1fb131c0d4fb7/pysam-0.15.1.tar.gz
    Complete output from command python setup.py egg_info:
    '.' 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: cython is available - using cythonize if necessary
    # pysam: htslib mode is shared
    # pysam: HTSLIB_CONFIGURE_OPTIONS=None
    # pysam: htslib configure options: None
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\mlsyring\AppData\Local\Temp\pip-install-h3benh6k\pysam\setup.py", line 223, in <module>
        htslib_make_options = run_make_print_config()
      File "C:\Users\mlsyring\AppData\Local\Temp\pip-install-h3benh6k\pysam\setup.py", line 69, in run_make_print_config
        stdout = subprocess.check_output(["make", "-s", "print-config"])
      File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 389, in check_output
        **kwargs).stdout
      File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 466, in run
        with Popen(*popenargs, **kwargs) as process:
      File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 769, in __init__
        restore_signals, start_new_session)
      File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 1172, in _execute_child
        startupinfo)
    FileNotFoundError: [WinError 2] The system cannot find the file specified

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\mlsyring\AppData\Local\Temp\pip-install-h3benh6k\pysam\

I updated setuptools (as other forums mentioned) with pip install --upgrade setuptools, but I still get the error. Any idea how to fix this? I can get other packages to install, just not nanopack.

wdecoster commented 5 years ago

Thanks for reporting this. I have a couple of questions:

Cheers, Wouter

KidneyPunch commented 5 years ago
wdecoster commented 5 years ago

not sure about the windows subsystem... I tried installing pysam on it's own, but same error. Maybe I need to troubleshoot with them...

But you are using windows? Pysam is known to have issues on Windows. On Windows 10 you can install Ubuntu, for more information see here, and that should work.

I was wanting to use NanoLyse to remove the control sequence, but wanted to check out the entire package too.

For NanoLyse you can also use pip install NanoLyse.

KidneyPunch commented 5 years ago

OK, I'll use that for now to install NanoLyse on it's own, then contact Pysam for more info. Thanks for your help & responsiveness!