picard

Versions: [2.24.0, 2.25.0, 2.25.1, 2.25.2, 2.25.3, 2.25.4, 2.25.5, 2.25.6, 2.25.7, 2.26.0, 2.26.2]

picard

Download        : docker pull ghcr.io/autamus/picard
Compressed Size : 235MB

Description

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Usage

Pull (Download)

To download the latest version of picard run,

docker pull ghcr.io/autamus/picard:latest

or to download a specific version of picard run,

docker pull ghcr.io/autamus/picard:2.24.0

Run

To run the container as an application run,

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

or to run the container in an interactive session run,

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

Mounting volumes between the container and your machine

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