HIBF Benchmarks

🚧 Work in progress 🚧

Quickstart

Edit configuration

• General configuration: config/config.yaml
• Plot configuration: config/plot_config.yaml
• Meta information: workflow/scripts/bokeh_plot/components/plot_css_html.py

Setup

• Conda or Mamba
• Snakemake

# Create an environment called `snakemake` with snakemake installed
conda env create --channel conda-forge --name snakemake bioconda::snakemake

Run

conda activate snakemake
snakemake --use-conda --cores 2

The results can be found in results/html/index.html.

Testing/Running without Raptor

To test the workflow without running Raptor, data is provided in .github/data:

# run from repository root directory
mkdir --parents results/raw_data
tar xf .github/data/data.tar.zst --directory=results/raw_data
export CI=true # Skips running raptor
snakemake --use-conda --cores 2 --forceall