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¶

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

Cyberduck¶

Download and install Cyberduck
Download the CyVerse configuration profile .
1. Double-click on the downloaded file - this should open the installed Cyberduck software.
Enter your CyVerse username in the field ‘iPlant username’.
Under ‘Advanced Options’ set ‘Transfer Files’ to ‘Open Multiple Connections’.
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¶

Download and install iCommands following the instructions for Linux , Mac, or Windows
Set path for i-command binaries:
1. Mac example: export PATH="/Applications/icommands/:$PATH"
2. Linux example: export PATH="/home/elyons/bin/:$PATH"
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:``

ils get list of files in current working directory in the Data Store
icd <directory> change working directory in the Data Store
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)

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)

WebDAV mount¶

Note: this is for a Mac

Open Finder
From the menu at the top of your screen, select “Go”
In the dropdown menu, select “Connect to Server…”
In the popup window called “Connect to Server” type in https://data.cyverse.org/dav/iplant/home/<your CyVerse user name>`
Another window will pop up. For “Connect As:” select “Registered User”. Type in your CyVerse user name for “Name:” and your CyVerse password for “Password”
If you logged in successfully, your data store account will be available through Finder. “data.cyverse.org” will be listed under “Locations” on the right menu in a Finder window

Summary¶

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

Additional information, help¶

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