ATLAS-Docker

Introduction

Docker image for ATLAS, the Analysis Tools for Low coverage and Ancient Samples. ATLAS is developped by Daniel Wegmann's Lab. ATLAS benefits from a highly dynamic team, and a fast developpement cycle. However, this results in issues if you are trying to run the latest and greatest code from the ATLAS team on your local HPC.

Here I provide a docker file that pulls the latest version of the code from ATLAS's bitbucket repository, builds all the requirements, and compiles the code.

Running the Docker image

Docker

You can use docker to run the ATLAS container on your Mac, Windows, or Linux based system:

docker run --mount type=bind,source=`pwd`,target=/Data thesmiao/atlas:beta1 atlas task=recalBAM verbose

Singularity

On an HPC where you don't have admin permissions, you can use Singularity to run ATLAS:

singularity exec -B `pwd` docker://thesmiao/atlas atlas task=recalBAM

Note: Make sure that Singularity on your HPC allows you to bind a given location, if you it doesn't work please contact your admin to edit the singularity configuration to allow you to do so.

ATLAS Documentation

For details on how to use the different modules of ATLAS refere to the project's wiki: https://bitbucket.org/wegmannlab/atlas/wiki/Home