fraggenescan

Download        : docker pull ghcr.io/autamus/fraggenescan
Compressed Size : 66MB

Description

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

Usage

Pull (Download)

To download the latest version of fraggenescan run,

docker pull ghcr.io/autamus/fraggenescan:latest

or to download a specific version of fraggenescan run,

docker pull ghcr.io/autamus/fraggenescan:1.31

Run

To run the container as an application run,

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

or to run the container in an interactive session run,

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

Mounting volumes between the container and your machine

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