abyss
Download : docker pull ghcr.io/autamus/abyss
Compressed Size : 80MB
Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.
Usage
Pull (Download)
To download the latest version of abyss run,
docker pull ghcr.io/autamus/abyss:latest
or to download a specific version of abyss run,
docker pull ghcr.io/autamus/abyss:2.2.5
Run
To run the container as an application run,
docker run --rm ghcr.io/autamus/abyss abyss --version
or to run the container in an interactive session run,
docker run -it --rm ghcr.io/autamus/abyss bash
Mounting volumes between the container and your machine
To access files from your machine within the abyss container you’ll have to mount them using the -v external/path:internal/path
option.
For example,
docker run -v ~/Documents/Data:/Data ghcr.io/autamus/abyss abyss /Data/myData.csv
which will mount the ~/Documents/Data
directory on your computer to the /Data
directory within the container.
HPC
If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC abyss container here.