README.md.j2

## BioAnalyze Docker Images

These docker images are built to use as a part of a full stack Bioinformatics Analysis Environment. Each image can be used on it's own or as a part of a Jupyterhub Cluster.

Each image is meant to be a full fledged ecosystem for Bioinformatics. Images:

* Are fully ready to use with a [Jupyterhub](https://zero-to-jupyterhub.readthedocs.io/en/latest/) or [Dask Gateway Cluster](https://gateway.dask.org/install-kube.html).
* RStudio installed
* Jupyterlab installed
* Common software packages for data science such as Pandas, SciKit Learn, and TidyVerse
* Bioinformatics workflow runners: [Snakemake](https://snakemake.readthedocs.io/en/stable/) and [Nextflow](https://www.nextflow.io/).
* Workflow Orchestration systems: [Prefect](https://docs.prefect.io/#basic-installation) and [Airflow](https://airflow.apache.org/docs/apache-airflow/stable/start/local.html).
* Use the excellent [Pangeo Project](https://github.com/pangeo-data/pangeo-docker-images) as a base.
* Documentation packages such as [Jupyterbook](https://jupyterbook.org/) and [RBookdown](https://bookdown.org/).

[Bioinformatics Ecosystem](./docs/_source/_static/images/BioHub-Ecosystem-IDEs-and-Development-Environment.jpeg)

See each of the images at [Dockerhub](https://hub.docker.com/orgs/dabbleofdevops/repositories).

Please note that this project is still under rapid development and the system used for tagging is likely to change.

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## Dask-gateway compatibility

(This information is completely grabbed from [Pangeo](https://github.com/pangeo-data/pangeo-docker-images#dask-gateway-compatibility))

If deploying in a Jupyterhub on Kubernetes cluster you'll need to make sure you're using the same pangeo versions.

| dask-gateway |  Pangeo Version tag  |
|--------------|-------------|
| 0.9          | 2020.11.06  |
| 0.8          | 2020.07.28  |
| 0.7          | 2020.04.22  |