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Introduction to CyVerse Self-Guided Course: CyVerse UK

Goal

This is a short self-guided course that will take you through the basics of using CyVerse.

Tip

See other versions of this documentation (CyVerse USA and CyVerse Austria)

In the lower-left hand side of the screen, change the version of this documentation from cyverse-us to one of the other documentation sets developed for this online guide (cyverse-usa or cyverse-at) to see specifics that apply to those installations.

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Tutorial Maintainer(s)

Who to contact if this guide needs fixing. You can also email learning@CyVerse.org

Maintainer	Institution	Contact
Krister Jazz Urog	CyVerse UK/ Earlham Insitute	KristerJazz.Urog@earlham.ac.uk

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• Tutorial home
• Course Overview
  • Create a CyVerse Account
  • Access and Search the CyVerse Learning Account
    • Self Assessment Questions
• CyVerse Background
  • CyVerse Background Videos and Slides
    • Self Assessment Questions
• Data Management I
  • Downloading data from the Discovery Environment
    • Self Assessment Questions
• Tour of the Discovery Environment
  • Self-guided Discovery Environment Tour
    • Self Assessment Questions
• Data Management II
  • Upload data with Cyberduck
  • Upload data using the Discovery Environment
    • Self Assessment Questions
• Analysis with the Discovery Environment
  • Descriptive Steps
    • Self Assessment Questions
• Data Management III
  • Descriptive Steps
    • Self Assessment Questions
• Interactive Analyses
  • Getting VICE Access
  • Launching a VICE application
  • Completing our analysis in R
  • Terminating your VICE session and saving work to the Data Store
    • Self Assessment Questions
• Conclusion and Advanced Applications
  • Descriptive Steps
  • Additional information, help
• Delete this example guide page
  • Many of the examples Writing your documentation using sample data
  • Using in-line questions with tips
  • Other admonitions
  • Buttons and keyboard combinations
  • URLs/Links
  • Images

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite	Preparation/Notes	Link/Download
CyVerse account	You will need a CyVerse account to complete this exercise	CyVerse User Portal
Atmosphere access	You must have access to Atmosphere	CyVerse User Portal
Cyberduck	Standalone software for upload/download to Data Store	Download Cyberduck

Platform(s)

We will use the following CyVerse platform(s):

Platform	Interface	Link	Platform Tour
Data Store	GUI/Command line	Data Store	Data Store Guide
Discovery Environment	Web/Point-and-click	Discovery Environment	Discovery Environment Guide

Application(s) used

Discovery Environment App(s):

App name	Version	Description	App link	Notes/other links
Muscle	3.8.31	Multiple sequence aligner		Original App Documentation

Atmosphere Image(s):

Image name	Version	Description	Link	Notes/other links
CyVerse CentOS 6.8 GUI Base	1.0	base image CentOS 6.8 with GNOME GUI

Input and example data

In order to complete this tutorial you will need to have the following inputs prepared

Input File(s)	Format	Preparation/Notes	Example Data

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Fix or improve this documentation

• Search for an answer: CyVerse Learning Center

• Ask us for help: click on the lower right-hand side of the page

• Report an issue or submit a change: Github Repo Link

• Send feedback: learning@CyVerse.org

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