Slivka-Bio Docker

This repository contains the Docker configuration for setting up slivka-bio.

Overview

slivka-bio is a pre-configured instance of a slivka server bundled with tools for bioinformatics applications. This Dockerized setup includes slivka-bio and MongoDB for data storage.

You can find out more about what slivka is and how to use it:

• at our public server hosted at the University of Dundee.
• on GitHub at the Slivka-bio and Slivka repositories.
• in the Slivka documentation.

Prerequisites

• Docker
• Docker Compose

Installation

To get started with slivka-bio-docker:

1. Clone the Repository

   git clone https://github.com/bartongroup/slivka-bio-docker.git
   cd slivka-bio-docker

2. Build and Run with Docker Compose

   docker-compose up -d

This will build the slivka-bio image and start all the services as defined in the docker-compose.yml.

Configuration

• The settings.yml file contains the configuration for slivka-bio. Adjust it as necessary for your environment.

Usage

After starting the services, the slivka-bio API documentation will be accessible via:

• URL: http://localhost:8080/api/ (or the appropriate domain/IP address)

MongoDB is also started and configured to work with slivka-bio.

For users looking to interact with slivka-bio from Python environments, including Jupyter notebooks, check out the Python client to get started.

Contributing

Contributions to this project are welcome! Please fork the repository and submit a pull request with your changes.

License

This project is licensed under the Apache-2.0 License. See the LICENSE file for details.

Funding

• This project was developed as part of the BBSRC funded Dundee Resource for Protein Structure Prediction and Sequence Analysis (grant number 208391/Z/17/Z).