wiki:GIMIv1.1Tutorial/Fromirods

Version 9 (modified by zink@cs.umass.edu, 7 years ago) (diff)

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F. Pull from iRODS

Image Map

F.1 iRODS Environment Settings

If ou haven't already performed this step in A.1, you first have to configure the your local iRODS environment:

  • The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
    # iRODS personal configuration file.
    #
    # This file was automatically created during iRODS installation.
    #   Created Thu Feb 16 14:06:27 2012
    #
    # iRODS server host name:
    irodsHost 'emmy9.casa.umass.edu'
    # iRODS server port number:
    irodsPort 1247
    
    # Default storage resource name:
    irodsDefResource 'iRODSUmass'
    # Home directory in iRODS:
    irodsHome '/geniRenci/home/gimiXX'
    # Current directory in iRODS:
    irodsCwd '/geniRenci/home/gimiXX'
    # Account name:
    irodsUserName 'gimiXX'
    # Zone:
    irodsZone 'geniRenci'
    

  • First of all copy the template iRODS configuration file to .irodsEnv with the following command:
    $ cp ~/Tutorials/GIMI/gimiXX/gimiIrodsEnv ~/.irods/.irodsEnv
    
  • Open ~/.irods/.irodsEnv with your favorite text editor (we recommend nano) and change gimiXX to your assigned username (e.g., gimi04).
  • Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
    $ iinit
    

  • You will be prompted for a password. Please type in the password you were provided with on the paper handout!!

F.2 Retrieving Data from iRODS to Local System

In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your local storage:

  • List content of your home directory
    ils
    
  • Retrieve file from your iRODS home directory into user workspace.
    $ iget <file_name>
    

Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:

$ iget gimitesting.sq3

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