abyss

Versions: [2.2.5, 2.3.0, 2.3.1]

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.