wiki:GIMIv1.1Tutorial/Fromirods

Version 8 (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

  • 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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