F. Pull from iRODS

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!!

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F.2 Retrieving Data from iRODS to Local System

• 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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