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Data Management II

Learning Objectives

  • Properly configure Cyberduck
  • Understand how Cyberduck works
  • Upload a dataset using Cyberduck to CyVerse

Description: In this module, we discuss how you can upload and download your dataset(s) in the Discovery Environment. This is done using Cyberduck, a 3rd party software that connects your local computer to the Data Store to enable drag-and-drop download and upload of data.

Input Data

Location File Example
On CyVerse README.txt View the example folder
On your Computer DE_sample_plants.fas

Setting up Cyberduck

  1. Download and install CyberDuck for your operating system.

  2. Download the CyVerse Cyberduck connection profile Double-click on the downloaded file (should be in your browser downloads)- this should open the now installed Cyberduck software.

  3. In the Cyberduck configuration window, enter your CyVerse username in the field iPlant username.

  4. Under Advanced Options ensure ‘Transfer Files’ option is set to ‘Open Multiple Connections’. Close this window - your entries will be automatically saved.

Username & multiple connections

Double-click on the Data Store bookmark in the window.

Set the bookmark

You should now be connected to the Data Store and viewing the contents of your home directory.

your home path is: /iplant/home/<username>

Upload data to the Data Store with CyberDuck

  1. Locate the raw_data folder inside your tutorial_folder in the Cyberduck display of your home directory.

  2. Upload the file DE_sample_plants.fas to the raw_data folder inside the tutorial_folder by dragging and droping.

  3. Back in the Discovery Environment, click the (Data Icon) to access your home folder.

  4. Navigate to the raw_data folder inside your tutorial_folder in your browser to verify the upload was successful.

Output/Results

Location File Example
On CyVerse README.txt & DE_sample_plants.fas View the example folder

Self Assessment Questions

Why do you need Cyberduck?

A To conveniently chat with CyVerse support

B To conveniently download and upload files from your local computer

C To conveniently create teams on the Discovery Environment

D To view apps and tools on the Discovery Environment

Answer

Correst answer is B.

Which of these will you need to configure and access the datastore using Cyberduck? Select all that apply:

A SSH access

B CyVerse account

C CyVerse Cyberduck connection profile

D Discovery Environment

Answer

Correct answer are B & C.

Download the CyVerse Cyberduck connection profile

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