Install HTSeq with Conda on Windows

[afDeathscythe]

Hi is there any chance to install the new version on Windows:

If I execute this Statement: pip install HTSeq

in Anaconda prompt as Admin I get this Error Message:

Collecting HTSeq Using cached https://files.pythonhosted.org/packages/f8/87/85bc27f3d96ff4cd9144cbbfb5eb7573654edd0f6970f5c49d15a17e5d6f/HTSeq-0.10.0.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. Traceback (most recent call last): File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 154, in save_modules yield saved File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 195, in setup_context yield File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 250, in run_setup _execfile(setup_script, ns) File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 45, in _execfile exec(code, globals, locals) File "C:\Users\dhg8103\AppData\Local\Temp\easy_install-nj3cyveq\pysam-0.14.1\setup.py", line 223, in File "C:\Users\dhg8103\AppData\Local\Temp\easy_install-nj3cyveq\pysam-0.14.1\setup.py", line 69, in run_make_print_config

Update version from VERSION file into module

  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 336, in check_output
    **kwargs).stdout
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 403, in run
    with Popen(*popenargs, **kwargs) as process:
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\dhg8103\AppData\Local\Temp\pip-install-lcnym_i4\HTSeq\setup.py", line 200, in <module>
    **kwargs
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\__init__.py", line 128, in setup
    _install_setup_requires(attrs)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\__init__.py", line 123, in _install_setup_requires
    dist.fetch_build_eggs(dist.setup_requires)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\dist.py", line 504, in fetch_build_eggs
    replace_conflicting=True,
  File "D:\Anaconda\anaconda3\lib\site-packages\pkg_resources\__init__.py", line 774, in resolve
    replace_conflicting=replace_conflicting
  File "D:\Anaconda\anaconda3\lib\site-packages\pkg_resources\__init__.py", line 1057, in best_match
    return self.obtain(req, installer)
  File "D:\Anaconda\anaconda3\lib\site-packages\pkg_resources\__init__.py", line 1069, in obtain
    return installer(requirement)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\dist.py", line 571, in fetch_build_egg
    return cmd.easy_install(req)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\command\easy_install.py", line 673, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\command\easy_install.py", line 699, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\command\easy_install.py", line 884, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\command\easy_install.py", line 1152, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\command\easy_install.py", line 1138, in run_setup
    run_setup(setup_script, args)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 253, in run_setup
    raise
  File "D:\Anaconda\anaconda3\lib\contextlib.py", line 99, in __exit__
    self.gen.throw(type, value, traceback)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 195, in setup_context
    yield
  File "D:\Anaconda\anaconda3\lib\contextlib.py", line 99, in __exit__
    self.gen.throw(type, value, traceback)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\_vendor\six.py", line 685, in reraise
    raise value.with_traceback(tb)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 154, in save_modules
    yield saved
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 195, in setup_context
    yield
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "D:\Anaconda\anaconda3\lib\site-packages\setuptools\sandbox.py", line 45, in _execfile
    exec(code, globals, locals)
  File "C:\Users\dhg8103\AppData\Local\Temp\easy_install-nj3cyveq\pysam-0.14.1\setup.py", line 223, in <module>
  File "C:\Users\dhg8103\AppData\Local\Temp\easy_install-nj3cyveq\pysam-0.14.1\setup.py", line 69, in run_make_print_config
    # Update version from VERSION file into module
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 336, in check_output
    **kwargs).stdout
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 403, in run
    with Popen(*popenargs, **kwargs) as process:
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "D:\Anaconda\anaconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
symlinking folders for python3
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None

I don't have any clue how set the specific symlinking folders for python3 (google solutions did not help me)

If I download the HTSeq-0.10.0.tar.gz and try to execute pip install setup.py (also in Anaconda Prompt) I get follwing error:

Collecting setup.py Could not find a version that satisfies the requirement setup.py (from versions: ) No matching distribution found for setup.py

Thanks & Regards,

Marko

[iosonofabio]

Thanks Marko. The answer is probably not.

1. I have no Windows machine nor am experienced enough with PowerShell to set one up in the cloud for this.
2. I use no conda myself, so I can't support it.

However, I'm happy to support windows in principle if anyone sets up a git branch that uses AppVeyor as a CI/CD system for HTSeq. In fact, I even started such branch but couldn't quite figure out the intricacies of Windows shelling to get it done. This will probably involve some work on Pysam too as I don't think they support much windows either (last time I checked - this might have changed).

So if you wanna see it happen, please fork the repo and make it happen, I'll try to help you as much as I can given the limitations above.

[afDeathscythe]

Hi Fabio,

thanks for replying. I am working with HTseq since 3 years now and I don't have time to investigate more on the windows issue to get it running there. I would be pleased to help and if find out something related to the known pysam issue I will let you know.