stuartmac/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. Pull the slivka-bio Docker image:

   docker pull stuartmac/slivka-bio
   

   Copy

2. Clone the repository and navigate to the directory:

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

   Copy

3. Start the services with Docker Compose:

   docker compose up -d
   

   Copy

   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.

⁠Running on ARM / Apple Silicon (M‑Series)

The Slivka image is built for multiple architectures, so docker pull will automatically download the image matching your platform. On Apple Silicon (M‑Series) Macs or other ARM64 systems, the default image runs natively and includes the Slivka server and a subset of the Slivka Bio tools. Some tools were not available for ARM at the time of the build.

If you need the full set of Slivka Bio tools on ARM, you can run the amd64 variant of the image under emulation. There are two ways to do this:

• Specify the platform when pulling or running the image:

  docker pull --platform=linux/amd64 stuartmac/slivka-bio
  docker run --platform=linux/amd64 …
  

  Copy

  This tells Docker to pull the x86_64 (amd64) version and run it under emulation (using QEMU on Mac).

• Use the provided docker-compose.arm64.yml:

  The slivka-bio-docker repository⁠ includes a docker-compose.arm64.yml file that sets the platform: linux/amd64 option for the services. Use this compose file on ARM machines to start the x86_64 image with all tools installed:

  docker compose -f docker-compose.arm64.yml up -d
  

  Copy

Using the amd64 image under emulation will provide access to all Slivka Bio tools but may have a performance impact compared to the native ARM build.

⁠Access the API

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

URL: http://localhost:8080/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).