HTSeq installation problem

Question

[cyberfofana]

Hello to all, I'm new in RNA-Seq data analysis. I want to install HTSeq on windows 10 after installation of Python 2.7 and pip 18.1 but I have somme problems.

pip install HTSeq
Collecting HTSeq   
Using cached https://files.pythonhosted.org/packages/b1/55/3612dc17fe2a85c9f0a4b98b97aa8a9850d0930e2ad89deaf9c5e1271e97/HTSeq-0.11.2.tar.gz
    ERROR: Complete output from command python setup.py egg_info:
    ERROR: symlinking folders for python2
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "c:\users\public\documents\wondershare\creatortemp\pip-install-ztzvdn\HTSeq\setup.py", line 20, in <module>
        os.symlink(py_fdn+fdn, fdn)
    AttributeError: 'module' object has no attribute 'symlink'
    ---------------------------------------- ERROR: Command "python setup.py egg_info" failed with error code 1

Someone can help me please ?

[WouterDeCoster]

Why don't you use the Windows Subsystem for Linux (WSL)?

Answer 1

[ATpoint]

Please read the manual and use the search function ( Problem installing HTSeq on Windows 10 ):

At the moment, HTSeq supports Linux and OSX but not Windows operating systems, because one of the key dependencies, Pysam, lacks automatic support and none of the HTSeq authors have access to such a machine. However, it might work with some work, if you need support for this open an issue on our Github page.

Answer 2

[Devon Ryan]

You need to use python3 on windows, os.symlink() only works on OSX and Linux with python 2. You'll be better off with featureCounts though, which is both faster and more likely to run on windows.

[cyberfofana]

I used featureCounts but don't gave me satisfaction. I will try with python3. But in documentation and on official HTSeq site, autors said that it works on windows with Python 2.7.

[WouterDeCoster]

I used featureCounts but don't gave me satisfaction.

What does that mean?