Pip installation fails on PyVCF

[haochenz96]

Hi,

Thanks for developing this amazing tool!

While I tried to install it with pip today, I got an error saying:

Collecting pyvcf
  Downloading PyVCF-0.6.8.tar.gz (34 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      error in PyVCF setup command: use_2to3 is invalid.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

I believe this is related to PyVCF not compatible with setuptools used in newer Python (mine is Python 3.7.12), as mentioned in this issue: jamescasbon/PyVCF#332

Also, it seems that PyVCF only parses VCF format V4.0 and V4.1, whereas the standard right now is V4.2. The package does not seem to be maintained anymore. So it may be better to switch to a newer VCF parser.

Haochen

[rkimoakbioinformatics]

@haochenz96 Thanks for letting us know. It is indeed a known problem. First of all, a workaround is:

>pip install "setuptools<58" --upgrade
>pip uninstall pyvcf
>pip install pyvcf

VCFPy seems to be an alternative. If it proves to be better than PyVCF, it'll be used instead of PyVCF.

[haochenz96]

Ok. Thanks. I seem to have got around it in another way: I just installed it with

conda install -c bioconda open-cravat

Will try it out and let you know if the PyVCF parser has any issue

[rkimoakbioinformatics]

Ok great. Closing the thread for now.

[BenjaminDEMAILLE]

Same error

[jasminebro]

Same error

Hi @BenjaminDEMAILLE . Are you having the same error currently?

[BenjaminDEMAILLE]

Yes with Python 3.12

…

Le 16 déc. 2024 à 14:25, Jasmine Baker ***@***.***> a écrit : Same error Hi @BenjaminDEMAILLE <https://github.com/BenjaminDEMAILLE> . Are you having the same error currently? — Reply to this email directly, view it on GitHub <#98 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ6MVUE6DMU3AJU5J5VYMPL2F3IE7AVCNFSM6AAAAABTV276BWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBVGYZDQMRVGU>. You are receiving this because you were mentioned.

[kmoad]

@BenjaminDEMAILLE I'm getting clean installs. Could you please share:

• What OS you're using
• How you have python installed (native, anaconda, docker, etc)
• The output of running pip install open-cravat