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Data Download

Description: Managing your data on CyVerse

Official CyVerse Data Management

Using CyVerse iCommands

Official iCommands User

Data Sharing Services:

Cyverse_data_services

Input Description Link
Google Drive Cloud Data Storage Service Jupyter Client
Cyverse Data Store integrated Rule-Oriented Data System (iRODS) Jupyter Client
CyberDuck File Share UI Using with CyVerse
Guacamole Atmosphere Browser Tabs  

Google Drive Jupyter Client

Note

As of July 2018, the Google Drive Jupyter Client has been deprecated.

Update Conda to latest

conda update conda
conda update conda-build

Dependency: Node.js 5+

conda install -c conda-forge nodejs
  1. Install Google Drive to Jupyter Lab

Google Drive requires port 8888 or 8889 with port forwarding to work

jupyter labextension install @jupyterlab/google-drive

iRODS Jupyter Client

CyVerse has a developed a Jupyter Lab iRODS client similar to the Google Drive extension.

Update to the latest version of Jupyter Lab

conda install -c conda-forge jupyterlab

pip install jupyterlab_irods
jupyter serverextension enable --py jupyterlab_irods
jupyter labextension install @towicode/jupyterlab_irods

iRODS iCommands CLI

CyVerse Instructions

Instructions from iRODS

Download from iRODS

  1. Install iCommands on the VM

    wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
sudo apt-get update
sudo apt-get install irods-icommands

  2. Initialize iRODS-iCommands

    iinit

You will be queried to set up your irods_environment.json

Enter the following:

statement input
DNS data.cyverse.org
port 1247
username your CyVerse username
zone iplant

Note

Set up auto-complete for iCommands instructions

Download i-commands-auto.bash

In your home directory, rename i-commands-auto.bash to .i-commands-auto.bash

In your .bashrc or .bash_profile, enter the following:

source .i-commands-auto.bash

CyberDuck

CyberDuck is a GUI client that works in Windows and Mac OS X. It can connect to almost every type of proximate file sharing system (DropBox, Drive, AWS S3, SFTP, iRODS, etc).

Using CyVerse and CyberDuck

CyberDuck also has a CLI client that can be used in Linux.

To install on the VM:

echo -e "deb https://s3.amazonaws.com/repo.deb.cyberduck.io stable main" | sudo tee /etc/apt/sources.list.d/cyberduck.list > /dev/null
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys FE7097963FEFBE72
sudo apt-get update
sudo apt-get install duck

Guacamole

Open the Web Desktop or Web Shell from the Atmosphere UI

Ctrl + Alt + Shift to open the side bar.

Click on Devices

Select the Home folder (or a folder that your $USER has ownership of) and upload data.

Description of output and results

Congratulations! You’ve established ways to get data to and from your VM!

Fix or improve this documentation

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