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](https://singularity-hub.org/) / [Docker](https://hub.docker.com/) containers in the cloud, we recommend [Atmosphere](https://www.cyverse.org/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.**

![](/img/cloud_computing.png)

> [**1. Register for a free account on CyVerse here**](https://user.cyverse.org/register)

> [**2. Follow this Guide to Launching Atmosphere Instances**](https://snakemake2019.readthedocs.io/en/latest/Atmosphere_Cloud.html)

> [**3. Click here for Snakemake Tutorial on Atmosphere**](https://snakemake2019.readthedocs.io/en/latest/smake_cloud_tutorial.html)

> 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**](https://www.cyverse.org/about) 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.

+ [CyVerse Allocations Wiki](https://wiki.cyverse.org/wiki/display/atmman/Requesting+More+Atmosphere+Resources)

> [**Jetstream**](https://jetstream-cloud.org/) 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.

> [**1. Register for an account on XSEDE User Portal**](https://portal.xsede.org/web/xup/my-xsede?p_p_id=58&p_p_lifecycle=0&p_p_state=maximized&p_p_mode=view&saveLastPath=0&_58_struts_action=%2Flogin%2Fcreate_account)

+ [Jetstream Allocations Wiki](https://iujetstream.atlassian.net/wiki/spaces/JWT/pages/76149919/Jetstream+Trial+Access+Allocation)