Installation

ASOkai needs Python 3.10 to 3.12 and the external programs KMC and Bowtie 2.

With Conda

Conda installs KMC and Bowtie 2 alongside the Python dependencies, on Linux and macOS:

conda env create -f environment.yaml
conda activate ASOkai
python -m pip install -e .

Replace the last line with python -m pip install -e ".[dev]" to add the contributor tools: pytest, pyright, black, pre-commit, cwltool, and Sphinx.

Windows

Bioconda publishes no Windows packages, so KMC and Bowtie 2 cannot come from the Conda environment there. Instructions for installing them separately will be added.

Verify

asokai list steps

The command prints the installed steps. ASOkai is an equivalent command name.

Analyses that run on worker processes require fork and so use it only on Linux. Elsewhere they run on worker threads, which produces the same results and takes longer.

Next, the Getting Started guide configures and runs the pipeline.