Dependency Conflict: Installation of pyGenomeTracks Causes ResolutionImpossible Error

[im-habib]

Summary

There is a dependency conflict when attempting to install the required packages for the GeneMaster project using pip install -r requirements.txt. The error message indicates a conflict between pyGenomeTracks and other packages, specifically matplotlib.

Error Message

WARNING: Package 'pyGenomeTracks' has an invalid Requires-Python: Invalid specifier: '>=3.7.*'
ERROR: Cannot install -r requirements.txt (line 13), -r requirements.txt (line 8) and matplotlib>=3.9.0 because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

[lldelisle]

Hi @asmdhabibullah ,
I don't know the GeneMaster project but indeed, in the current version we do not support matplotlib 3.9 as we prefer to test it before allowing it.
I think there are 2 options for you:

• If you need pyGenomeTracks but not necessarily in the same environment as the other python packages you have, you can create a conda environment with pygenometracks: conda create -n pgt -c conda-forge -c bioconda pygenometracks=3.9 then conda activate pgt and then use it. Or a virtual environment with pygenometracks python -m venv ~/.pgt then . ~/.pgt/bin/activate then pip install pygenometracks==3.9 and then use it.
• If you really need pyGenomeTracks in the same environment, then you should clone the repository, modify this line

  pyGenomeTracks/pyproject.toml

  Line 21 in a644372

  "matplotlib >=3.1.1,<3.9",

  and do pip install . (no need to install the requirements, pip will take care of it).

[im-habib]

I'm not too fond of this solution :( cause I'm using "venv" environment, no conda

[lldelisle]

I gave you 3 solutions, only one is using conda.
Have you checked the third one?
If none is convenient for you, you need to wait for a new release.