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Data Store Quickstart

Goal: Simple steps to get setup with the CyVerse Data Store


Prerequisites

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

Platform(s)

We will use the following CyVerse platform(s):

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

Get started

CyVerse Discovery Environment

  1. Open a web browser
  2. Log into the CyVerse Discovery Environment: https://de.cyverse.org
  3. Press the “Data” icon on the left
  4. That opens the data management window
  5. The navigation bar on the left is where you navigate your folder, public folders, and folders/files shared with you
  6. The menu bar at the top is where you can:
    1. Upload/Download data
    2. Create folders
    3. Share data

Cyberduck

  1. Download and install Cyberduck
  2. Download the CyVerse configuration profile .
    1. Double-click on the downloaded file - this should open the installed Cyberduck software.
  3. Enter your CyVerse username in the field ‘iPlant username’.
  4. Under ‘Advanced Options’ set ‘Transfer Files’ to ‘Open Multiple Connections’.
  5. Double-click on the Data Store bookmark in the Cyberduck window. Enter your CyVerse credentials.

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


Command Line

  1. Download and install iCommands following the instructions for Linux or Mac
  2. Set path for i-command binaries:
    1. Mac example: export PATH="/Applications/icommands/:$PATH"
    2. Linux example: export PATH="/home/elyons/bin/:$PATH"
  3. Run iinit and configure irods environment

Example iinit:

elyons@air (~) $ iinit
One or more fields in your iRODS environment file (.irodsEnv) are
missing; please enter them.
Enter the host name (DNS) of the server to connect to:data.cyverse.org
Enter the port number:1247
Enter your irods user name:elyons
Enter your irods zone:iplant
Those values will be added to your environment file (for use by
other i-commands) if the login succeeds.

Enter your current iRODS password:``
  1. ils get list of files in current working directory in the Data Store
  2. icd <directory> change working directory in the Data Store
  3. iget <filename> will get files from the Data Store
$ iget -r # For recursive transfer of directories and their contents

$ iget -P # display the progress of the upload

$ iget -f # force the upload and overwrite

$ iget -T # Renew socket connection after 10 min (May help connections
          # that are failing due to some connection/firewall settings)
  1. iput <filename> iput will put files from local machine to the Data Store
$ iput -r # For recursive transfer of directories and their contents

$ iput -P # display the progress of the upload

$ iput -f # force the upload and overwrite

$ iput -T # Renew socket connection after 10 min (May help connections
          # that are failing due to some connection/firewall settings)

Summary

You now have the power to move data. Use your power wisely.


Additional information, help

Search for an answer: CyVerse Learning Center or CyVerse Wiki


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