Changes between Version 1 and Version 2 of GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Analyze


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Timestamp:
03/14/13 13:52:42 (11 years ago)
Author:
divyashri.bhat@gmail.com
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  • GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Analyze

    v1 v2  
    1 == F. Pull from iRODS ==
    2 
    3 {{{
    4 #!html
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    6 <img id="Image-Maps_2201210012154478" src="http://emmy9.casa.umass.edu/images/GIMI_workflow_F.jpg" usemap="#Image-Maps_2201210012154478" border="0" width="323" height="531" alt="" />
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    26 <!-- Image map text links - End - -->
    27 
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    29 }}}
    30 
    31 === F.1 iRODS Environment Settings ===
    32 If you haven't already performed this step in A.1, you first have to configure the your local iRODS environment:
    33 
    34 * The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
    35 {{{
    36 # iRODS personal configuration file.
    37 #
    38 # This file was automatically created during iRODS installation.
    39 #   Created Thu Feb 16 14:06:27 2012
    40 #
    41 # iRODS server host name:
    42 irodsHost 'emmy9.casa.umass.edu'
    43 # iRODS server port number:
    44 irodsPort 1247
    45 
    46 # Default storage resource name:
    47 irodsDefResource 'iRODSUmass2'
    48 # Home directory in iRODS:
    49 irodsHome '/geniRenci/home/gimiXX'
    50 # Current directory in iRODS:
    51 irodsCwd '/geniRenci/home/gimiXX'
    52 # Account name:
    53 irodsUserName 'gimiXX'
    54 # Zone:
    55 irodsZone 'geniRenci'
    56 }}}
    57  
    58   * First of all copy the iRODS configuration file to .irodsEnv with the following command (replace gimiXX with your username):
    59 {{{
    60 $ cp ~/Tutorials/GIMI/gimiXX/gimiXXIrodsEnv ~/.irods/.irodsEnv
    61 }}}
    62  * Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
    63 {{{
    64 $ iinit
    65 }}}
    66  
    67  * You will be prompted for a password. Please type in the password you were provided with on the paper handout!!
    68 
    69 ----
    70 
    71 === F.2 Retrieving Data from iRODS to Local System ===
    72 In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
    73 local storage:
    74 
    75   * List content of your home directory
    76 {{{
    77 $ ils
    78 }}}
    79   * To change to a different directory use
    80 {{{
    81 $ icd
    82 }}}
    83   * Retrieve file from your iRODS home directory into user workspace.
    84 {{{
    85 $ iget <file_name>
    86 }}}
    87 
    88   Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
    89 {{{
    90 $ iget gimitesting.sq3
    91 }}}
    92   * A complete overview on the iRODS commands can be found [https://www.irods.org/index.php/icommands here].
    93 
    94 === F.3 Searching the Catalogue for Data ===
    95 {{{
    96 $ imeta qu -d SliceName like gimi28
    97 }}}
    98 
    99 
    100 ----
    101 
    102 [[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/Analyze Back to previous step]]
    103 
    104 [[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/Cleanup Forward to next step]]
    105 
    106 [[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/ Back to tutorial main page]]