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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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Resolving Pysam Errors During GWASLab Installation #52

Open lphotoimpact opened 10 months ago

lphotoimpact commented 10 months ago

  1. I attempted to install GWASLab in WSL2 using the command pip install gwaslab==3.4.24.

  2. However, the installation failed due to issues with Pysam. I discovered that Pysam version 0.21, which is compatible with Python 3.11, was causing the problem.

  3. GWASLab required an older version of Pysam, specifically version 0.19.1. But attempting to install this older version also failed.

  4. In the end, I successfully installed GWASLab by creating a Python 3.8 environment in Anaconda.

If you encounter similar compatibility issues in the future, creating a compatible environment using Anaconda or virtual environments can be a suitable workaround to ensure successful installations. . . . On the other hand, when using Anaconda on Windows, even after creating a Python 3.8 environment, I still encountered Pysam installation failures.

a similar question: https://github.com/Cloufield/gwaslab/issues/9#issue-1645243411 The author's response in this question, "I guess the issue here might be pysam (or its dependencies like htslib) not supporting the Windows platform."

Therefore, I use WSL2.

Cloufield commented 10 months ago

Thanks for the suggestion. Actually, I prepared one which is ready to use: https://github.com/Cloufield/gwaslab/blob/main/environment.yml. I think some of the version requirements need to be further limited when building the package for PyPi. But for Windows platform, I guess using WSL is the only option for now.