Using Python in Pixi

You can also install Python packages into your Pixi environment. As an example we will use FastQE, a Python based tool that translates the fastq quality scores into emojis.

Prepare the environment

pixi init fastqe -c conda-forge
cd fastqe/
pixi add python
pixi add --pypi fastqe
pixi add --pypi setuptools

run FastQE on your sample(s)

pixi run srun -A project_ID -t 02:00 fastqe --html  --output sample_name.html ../sample1.fastq