GEMmaker uses a variety of bioinformatics software packages, which will be downloaded to your machine automatically. The GEMmaker workflow is downloaded automatically to your machine when you run it via Nextflow for the first time. To do this, there are two dependencies you will need: Nextflow and your choice of container executor (Singularity or Docker).

Required Dependencies

At a minimum, GEMmaker requires the following:

  • Nextflow : Executes the workflow. Nextflow also requires an installation of Java.
  • Singularity or Docker. (Singularity Recommended)

Container Support

All of the software tools needed to run GEMmaker have been pre-installed into a Docker container. Therefore, you do not need to install them! Using the container can ensure that results from GEMmaker are always reproducible because the environment in which the software is executed will not change even if the host computational computer is updated. Please ensure one of these containerization services are installed.

Choice of Computing Environment

Local Machine

GEMmaker can be run on a local computer; in particular, it has been tested on Ubuntu. GEMmaker has been optimized to allow for execution of large sample sizes without consuming large amounts of storage space. However, the time required to execute is dependent on the amount of computing power the machine has. You should consider using a High-Performance Computing (HPC) system if you have a large number of samples and would like GEMmaker to execute faster.

High-Performance Computing (HPC) Setup

On an HPC system it is recommended to use containerized dependencies as most HPC users do not have access to install software and HPC systems can change yielding results that may be hard to reproduce after time has passed and system setups have changed. Additionally, most HPC setups do not allow users to run Docker, but rather support Singularity instead. Using singularity is recommended on an HPC system rather than installing software dependencies manually. You will need to make sure that nextflow and Singularity are installed on your cluster (you may need the help of your HPC administrator).