bedops

Download        : docker pull ghcr.io/autamus/bedops
Compressed Size : 30MB

Description

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

Usage

Pull (Download)

To download the latest version of bedops run,

docker pull ghcr.io/autamus/bedops:latest

or to download a specific version of bedops run,

docker pull ghcr.io/autamus/bedops:2.4.35

Run

To run the container as an application run,

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

or to run the container in an interactive session run,

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

Mounting volumes between the container and your machine

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