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DATA STORE USER MANUAL
 

 

 

 

 

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About iCommands

iCommands is a collection of commands for Linux and Mac OS operating systems that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, in Linux you use ls , but in iCommands you use ils .

While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (2-100 GB each) and for bulk file transfers (many small files). For a comparison of the different methods of uploading and downloading data items, see Downloading and Uploading Data.

iCommands must be installed and configured for your system. Once set up, CyVerse users can use iCommands to access files that have been shared by other users, as well as manage metadata, change permissions on data files and folders you own, and more.

Even if you don't have an account, you can download public files using iCommands. For more information, see the iCommands section on the Downloading Data Files Without a User Account page. For information on using iCommands, see Using iCommands.

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For common Linux distributions, there are NetCDF iCommands available. Please see the NetCDF iCommands section.

For common Linux distributions, there are NetCDF iCommands available. Please see the NetCDF iCommands section for more information.

Setting up iCommands

iCommands must be set up and configured on each user's local machine or server, as outlined below, before you can transfer data to (with a CyVerse user account) and from the CyVerse Data Store using iCommands. Note that iCommands cannot be used to upload files into Data Store via URL from other sites (ftp, http, etc.). Without a CyVerse account, you can download public data from the Data Commons Repository (DCR).

For account users, you can download data from an external site using iCommands. To do so, download the file to a local machine using wget or a similar mechanism and then use iput to upload it to the Data Store. If you have a significant amount of external data to import from an external site, you may want to perform the transfer using a utility, such as Import by URL in the DE (not available using iCommands), or an Atmosphere instance.

Before you begin, you may want to watch a CyVerse video about iCommands.

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Because CyVerse products are interdependent with iRODS iCommands and iRODS products such as FUSE, the instructions for downloading iCommands vary according to your OS.

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Note
titleIMPORTANT! -- BEFORE YOU UPGRADE

Before upgrading to a 4.1 version, see Upgrading to iRODS 4.1 to view the list of services and testing done on the affected CyVerse offerings.

The most recent supported version for use with most CyVerse services is iRODS 4.1.10.

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titleNot sure which version you have?

To find the version you have installed, use ienv to find the client version or imiscsvrinfo to find the server version.

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yum install https://files.renci.org/pub/irods/releases/4.1.10/centos6/irods-icommands-4.1.10-centos6-x86_64.rpm

Next , continue to Step 2 to configure iCommands.

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Unprivileged Install
Unprivileged Install
Installation for Unprivileged Users

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  1. Download the correct installer.

    Tip
    titlealternate installers compatible with performance enhanced FUSE client

    If you intend to heavily use the iRODS FUSE client, it requires version 4.1.9 of the iCommands to be installed. Here are the installers for this version.

  2. From a terminal window, run the installer with  sh .

    For example, if you were installing iCommands on an Ubuntu 14.04 system as the user cyverse-user, you would do something like the following example. The iCommands would end up being placed in the directory /home/cyverse-user/icommands.

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    prompt> sh irods-icommands-4.1.10-ubuntu-14.installer
    Where would you like to install it? [/home/cyverse-user] 
    Expanding contents under /home/cyverse-user.
    Updating .bashrc
    done!
    
    To make the changes take effect in the current shell, please source your bashrc file, i.e., enter either `. ~/.bashrc`. or `bash`.

    Important: To make the changes take effect in the current shell, you will need to source your .bashrc file by entering either `. ~/.bashrc` .

    If you aren't using bash, or if your .bashrc file can't be edited, the environment variable IRODS_PLUGINS_HOME will need to be set to $INSTALL_BASE/icommands/plugins/ , where $INSTALL_BASE is the directory you provided to the installer. It is also recommended that you add the iCommands to your path.


  3. Open a new terminal window, if necessary, and run ienv to check that the new version was installed.

     

  4. Continue to Step 2 to configure iCommands.

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Mac OS

Warning

This Mac OS installer was tested for iCommands 4.1.9 compatibility with Mac OS 10.9 to 10.11 only.

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  1. Download the   Mac OS X iCommands 4.1.9 installer .
  2. Find the downloaded package, hold down the control button, and select the downloaded package.
  3. Click Open to give permission for Mac to open the package.
  4. Use the installer and follow the instructions .
  5. Open a new terminal window, if necessary, and run ienv to check that the new version was installed.
  6. Continue to Step 2 to configure iCommands.

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Microsoft Windows

iRODS does not currently offer a 4.1 download for Windows users. If you are running Windows 10, iCommands can be run on the Linux subsystem. See  https://docs.microsoft.com/en-us/windows/wsl/install-win10 for information on installing the Linux subsystem. Then follow the iCommands for Linux instructions to install iCommands.

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Step 2: Initialize/start the iRODS connection and configure the settings (One-time only or after changing your configuration)

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For the Linux distributions CentOS 6 and 7 and Ubuntu 12.04 and 14.04, there are three extra iCommands that support common NetCDF operations.  inc performs data operations on a list of NetCDF files. incarch archives a open ended time series data. incattr performs operation on attributes of NetCDF files. Each of these commands accepts the -h command line option. When a command is called with this option, it displays the command's help documentation.  Please see the this help documentation for more information.

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