Problem installing HTSeq on Windows 10

Question

[makwana.kd]

Hi Everybody, I am trying to install HTSeq on windows 10 64bit machine. I have tried using python command "pip install HTSeq", to get the following error:

C:\Python27\Scripts>pip install htseq
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting htseq
  Using cached https://files.pythonhosted.org/packages/b1/55/3612dc17fe2a85c9f0a4b98b97aa8a9850d0930e2ad89deaf9c5e1271e97/HTSeq-0.11.2.tar.gz
    Complete output from command python setup.py egg_info:
    symlinking folders for python2
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "c:\users\kuldeep\appdata\local\temp\pip-install-sfwygs\htseq\setup.py", line 20, in <module>
        os.symlink(py_fdn+fdn, fdn)
    AttributeError: 'module' object has no attribute 'symlink'

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in c:\users\kuldeep\appdata\local\temp\pip-install-sfwygs\htseq\

Alternatively, I tried downloading it on Anaconda3 using the command ," install -c bioconda htseq". It always says that the package is not found in the current channels.

[Arup Ghosh]

Have you tried conda install -c bioconda/label/cf201901 htseq ?

Ref

Answer 1

[ATpoint]

As you can see on the conda website for htseq (right below conda install ?) it is only available for OSX and Linux. Also, the htseq documentation (first hit when googling "htseq windows") states

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.

Either get a Linux or Mac machine or use a virtual machine to get either of the two running.

[makwana.kd]

Thank you ATpoint, I have installed it on Ubuntu.

Answer 2

[jared.andrews07]

Since you're on Windows 10, you should definitely use the Windows Subsystem for Linux, which makes bioinformatics much, much easier. I've yet to run into an issue with installing or using any tools with it.

I just installed htseq with no issues.

[makwana.kd]

Thank you Jared, Yes I missed that. I instead have installed it on Ubuntu. However, I am getting an error while running it on BAM file.

Error occured when reading beginning of SAM/BAM file. unsigned byte integer is greater than maximum Exception type: OverflowError, raised in libcutils.pyx:50

Is there a way to work around this error?