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Adding Packages

You may find that the analysis you would like to perform requires access to a software package that is not currently part of the mecfs_bioinformatics environment.

Adding PyPi Packages

If your software package is available on PyPi, you can add it with 

pixi add --pypi <your_package_name> --feature analysis

This will update pyproject.toml and pixi.lock by adding the package to the analysis dependency group (the main dependency group used by the project). You can use git add pyproject.toml pixi.lock; git commit -m '<your_message>' to add the environment update to your branch.

Adding bioconda/ conda-forge packages

If your package is instead present on bioconda or conda-forge, you can add it with

pixi add <your_package_name>  --feature analysis

Again, commit the resulting changes to pyproject.toml and pixi.lock.

Note that numerous Python packages are available on both PyPi and bioconda/ conda-forge. In such cases, it is preferable to install them from PyPi. Having Python packages installed from both sources can cause problems for Pixi's dependency resolver.