samtools

Versions: [1.12, 1.13]

samtools

Download        : docker pull ghcr.io/autamus/samtools
Compressed Size : 106MB

Description

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

Usage

Pull (Download)

To download the latest version of samtools run,

docker pull ghcr.io/autamus/samtools:latest

or to download a specific version of samtools run,

docker pull ghcr.io/autamus/samtools:1.12

Run

To run the container as an application run,

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

or to run the container in an interactive session run,

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

Mounting volumes between the container and your machine

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