iPlant Data Store Tutorial

iPlantDataStoreTutorial.markdown

(currently in progress)

#iPlant Data Store Tutorial

There are multiple ways to access files and directories on the iPlant Data Store (aka iRODS[1]). Here we will cover three methods, each with their pros and cons.

1. Browser-based Access --- User-friendly, but low throughput and 2GB upload limit
2. iCommands --- High throughput with maximum user control, but must be comfortable with the Command-Line Interface
3. iDrop --- High throughput and ability to schedule periodic transfers, but iDrop is in beta release and may have bugs

Regardless of which way you access your data, you need to know where it is located:
The path to a user's home directory is /iplant/home/username/ (replace "username").
The path to shared directories accessible by a user is /iplant/home/shared/.

If you don't have an iPlant account: You can register for your account at https://user.iplantcollaborative.org/register/. After registering, go to https://user.iplantcollaborative.org/dashboard/ to request access to the Atmosphere service by clicking on 'Request Access'.

##1. Browser-based Access

The iPlant Data Store can be accessed via your browser at https://data.iplantcollaborative.org or https://data.iplantc.org (you may get a warning that the latter link is attempting to redirect you to the former, but that's okay). The browser-based method of access is arguably the most intuitive way to access your iPlant data and requires the least amount of setup. However, there are two major limitations that accompany this convenience: (1) you cannot upload files >2GB and (2) it is difficult or impossible to manipulate or transfer multiple files at the same time via the browser.

####Navigation:

Quickly change to your home directory by clicking . To navigate to other directories, click on directory names or 'Parent Directory'. Be sure to click on the names and not the space to the right of the names. Clicking to the right of the names doesn't change directories, rather it selects the corresoponding file or directory for further manipulation.

####Uploading and downloading files

####Checking and modifying access permissions

####Sharing Files

Although you can alter permissions to allow other iPlant users to have access to your files, this doesn't help if you want to share files via the iPlant Data Store with colleagues that don't have an iPlant account. To share with the general public, select a file and click 'Share/Unshare'. After confirming your choice, you will see a URL to the right of the file name in the 'QuickShare' Column. You can share this URL with people and when they click it, the shared file will download. Sharing of a file can be stopped by selecting the file and clicking 'Share/Unshare' again. Entire directories cannot be shared in this manner, only individual files.

####Other types of file manipulation (creating directories; renaming, copying, moving, and deleting files/directories)

####Deleted Files

Deleted files remain (at least temporarily) in your trash folder until you empty the trash. Click on the to view these files. Here, you can 'Restore' deleted files or 'Empty Trash'.

##2. iCommands

iCommands allow you to manipulate the files and directories to which you have access on the iPlant Data Store.

####Installing and Configuring iCommands

• Download and install binaries
• Setup auto-complete (for Bash shell)
• Initiate an iRODS connection by typing: iinit

####iCommands Examples iCommands for transferring files are like their analogous commands, but more robust due to threading[2]:

• iput ≈ ftp put - upload
• iget ≈ ftp get - download
• irsync ≈ unix rsync - synchronize and keep up-to-date

Other Unix-like iCommands

• ils - list attributes of a file or the contents of a directory
• icp - copy
• imv - move or rename
• irm - remove/delete
• imkdir - make directories
• ipwd - print working directory
• ichmod - modify permissions

For more detailed usage information, click on the iCommands above, visit the iCommands website, or type the iCommand followed by -h in a Terminal window. For example, iput -h outputs the following:

Usage : ils [-ArlLv] dataObj|collection ...
Display data Objects and collections stored in irods.
Options are:

||| | --- | --- | | -A | ACL (access control list) and inheritance format | | -l | long format | | -L | very long format | | -r | recursive - show subcollections | | -v | verbose | | -V | Very verbose | | -h | this help|

iRODS Version 2.5 --- Feb 2011 --- ils

iput example

iPlant Data Store Cheatsheet

iPlant Data Store Quick Start

##3. iDrop

Normal iDrop - Allows access to user's home directory

"Expert" iDrop - Allows access to shared resources, too

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Footnotes:

1. iRODS...
2. Threading...

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last updated by mike covington --- 2012-03-28