24. Snakemake Tutorial on CyVerse cloud

Learning Objective
  • Cloud Computing
  • Launch and work on remote instances (virtual machines) with pre-built images
To run Snakemake jobs via Singularity / Docker containers in the cloud, we recommend Atmosphere, CyVerse’s cloud-computing platform which provides easy-to-use web-access to cloud resources and is designed to accommodate computationally and data-intensive tasks.

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The Snakemake2019 image supports: 1) Miniconda3 2) bio-conda 3) Snakemake 4) Singularity 5) Docker

Atmosphere / Jetstream Key Features:

  • Access virtual machine images pre-configured with an operating system and software to help you do scientific computations in domain-specific tasks
  • Find and use tools with the intuitive self-service portal
  • Easily manage virtual machines
  • Publish your own software suites, create your own work environments, and run the software for community use
  • Access your data in the Data Store, including high-performance computing (HPC) and grid computing environments
  • Integrate with existing infrastructure components using API services
  • Easily generate and manage statistical reporting of user resources for total CPU hours and memory usages, total instances and applications launched by user, cloud monitoring, and on-demand intelligence resource allocation
CyVerse is a cyber-infrastructure initiative funded by the National Science Foundation’s Directorate for Biological Sciences to address the growing needs for highly configurable and customized computational infrastructure to support research efforts in data sciences.
Jetstream is an [NSF/XSEDE] resource designed to promote and provide configurable cyberinfrastructure in the form of cloud computing to both novice and experienced users. Jetstream features a web-based user interface based on the popular Atmosphere cloud computing environment developed by CyVerse.