Closed raecv closed 2 years ago
Hi Raeline,
thanks for bringing up this issue and providing the details. I will see whether I can integrate this solution into the installation.
Cheers, Anna
I have added PyVCF separately to the installation requirements.
For the installation from yml, pyvcf is now installed via conda. For the pip installation, I had to downgrade pyvcf to version 0.4.3.
This has fixed the issue (at least for me), and the installation should now work with both options:
python -m pip install git+https://github.com/stjude/punctatools.git
conda env create -f punctatools.yml
Let me know if you still run into problems.
Encountered error message while installing or creating a punctatools environment on macOS Monterey Version 12.3.1, conda 4.13.0.
Running either of the following lines to install or create a punctatools env
python -m pip install git+https://github.com/stjude/punctatools.git
conda env create -f punctatools.yml --force
resulted in the following error: punctatools_env-error.txtThe main issue seems to be an error with the
use_2to3
command in PyVCF setup:Solution
This seems to be an error with the setuptools version as described here: [https://github.com/KarchinLab/open-cravat/issues/98], which can be fixed by building the punctatools conda env in the following way: