spades

Download        : docker pull ghcr.io/autamus/spades
Compressed Size : 107MB

Description

SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.

Usage

Pull (Download)

To download the latest version of spades run,

docker pull ghcr.io/autamus/spades:latest

or to download a specific version of spades run,

docker pull ghcr.io/autamus/spades:3.15.0

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/spades spades --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/spades bash

Mounting volumes between the container and your machine

To access files from your machine within the spades 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/spades spades /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 spades container here.