bedtools2
Download : docker pull ghcr.io/autamus/bedtools2
Compressed Size : 28MB
Description
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
Usage
Pull (Download)
To download the latest version of bedtools2 run,
docker pull ghcr.io/autamus/bedtools2:latest
or to download a specific version of bedtools2 run,
docker pull ghcr.io/autamus/bedtools2:2.30.0
Run
To run the container as an application run,
docker run --rm ghcr.io/autamus/bedtools2 bedtools2 --version
or to run the container in an interactive session run,
docker run -it --rm ghcr.io/autamus/bedtools2 bash
Mounting volumes between the container and your machine
To access files from your machine within the bedtools2 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/bedtools2 bedtools2 /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 bedtools2 container here.