plaquette/ska2 repository overview

⁠SKA Docker Container

This Docker container provides an environment with SKA (Simple K-mer Analysis Tool) installed, ready for running SKA commands. SKA is designed for the alignment and analysis of genomic data using k-mer based methods. The Docker image is based on Ubuntu 22.04 (Jammy Jellyfish) to ensure compatibility with the SKA binary's GLIBC requirements.

⁠Building the Docker Image

To build the Docker image from the Dockerfile, navigate to the directory containing the Dockerfile and use build_push.sh

⁠Running the Container

To run a container using the built image use demo.sh

This command starts an interactive bash session within the container. You can run SKA commands directly in this shell.

⁠Running SKA Commands

With the container running and your data directory mounted, you can execute SKA commands. For example:

ska align --min-freq 1 --filter no-filter /data/output/laos_ska_index.skf -o /data/output/laos_ska_alignment.aln --threads 4

Ensure your paths are adjusted to match where your files are located within the mounted directory.

⁠Further Information

For more details on SKA and its usage, visit the SKA GitHub repository⁠.