drsasp/slivka-bio repository overview

⁠slivka-bio: Ready-to-use bioinformatics web services with REST API

slivka-bio is a pre-configured bioinformatics server bundling tools like Clustal Omega, MAFFT, MUSCLE, and more. It simplifies the deployment of bioinformatics workflows via a REST API, using MongoDB as a backend.

This resource was developed by the Dundee Resource for Sequence Analysis and Structure Prediction⁠. For more details or to try our public server, visit the slivka-bio web server⁠.

⁠Quick Start

Ensure you have Docker and Docker Compose available on your system and follow the Docker Compose install docs⁠ if you haven't.

1. Clone the repository and navigate to the directory:

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

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2. Start the services with Docker Compose:

   docker compose up -d
   

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   Hint: If this command fails, try docker-compose (with a hyphen) on older systems.

Docker Compose manages both slivka-bio and MongoDB, ensuring that all dependencies are correctly set up and running.

⁠Access the API

Once the services are running, access the slivka-bio API at:

URL: http://localhost:4040/api/⁠ (or your server's domain/IP)

For further usage, including interacting with slivka-bio from Python or Jupyter notebooks, check out the Python client⁠.

⁠Use with Jalview 2-12

To configure Jalview⁠ to use your local slivka-bio instance for alignment and analysis services, see the installation instructions for Jalview Develop 2-12⁠, then add the base server URL in the Slivka Services pane in Preferences.

⁠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).