https://github.com/seqan/hibf_benchmarks
WIP HIBF benchmarks
https://github.com/seqan/hibf_benchmarks
Last synced: 4 months ago
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WIP HIBF benchmarks
- Host: GitHub
- URL: https://github.com/seqan/hibf_benchmarks
- Owner: seqan
- License: bsd-3-clause
- Created: 2023-12-11T16:05:36.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-11-24T13:23:50.000Z (7 months ago)
- Last Synced: 2026-02-11T02:26:36.371Z (4 months ago)
- Language: Python
- Homepage: https://seqan.github.io/hibf_benchmarks/
- Size: 243 KB
- Stars: 0
- Watchers: 5
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# HIBF Benchmarks
🚧 Work in progress 🚧
## Quickstart
### Edit configuration
* General configuration: [config/config.yaml](config/config.yaml)
* Plot configuration: [config/plot_config.yaml](config/plot_config.yaml)
* Meta information: [workflow/scripts/bokeh_plot/components/plot_css_html.py](workflow/scripts/bokeh_plot/components/plot_css_html.py)
### Setup
* [Conda](https://docs.anaconda.com/miniconda/miniconda-install) or [Mamba](https://github.com/conda-forge/miniforge?tab=readme-ov-file#install)
* [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
```bash
# Create an environment called `snakemake` with snakemake installed
conda env create --channel conda-forge --name snakemake bioconda::snakemake
```
### Run
```bash
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`:
```bash
# 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
```