Changes between Initial Version and Version 1 of GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Fromirods


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Timestamp:
03/14/13 13:51:18 (11 years ago)
Author:
divyashri.bhat@gmail.com
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  • GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Fromirods

    v1 v1  
     1== F. Pull from iRODS ==
     2
     3{{{
     4#!html
     5<div style="text-align:left; width:323px; margin-left:auto; margin-right:auto;">
     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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     24<area shape="rect" coords="321,529,323,531" href="http://www.image-maps.com/index.php?aff=mapped_users_2201210012154478" alt="Image Map" title="Image Map" />
     25</map>
     26<!-- Image map text links - End - -->
     27
     28</div>
     29}}}
     30
     31=== F.1 iRODS Environment Settings ===
     32If 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:
     42irodsHost 'emmy9.casa.umass.edu'
     43# iRODS server port number:
     44irodsPort 1247
     45
     46# Default storage resource name:
     47irodsDefResource 'iRODSUmass2'
     48# Home directory in iRODS:
     49irodsHome '/geniRenci/home/gimiXX'
     50# Current directory in iRODS:
     51irodsCwd '/geniRenci/home/gimiXX'
     52# Account name:
     53irodsUserName 'gimiXX'
     54# Zone:
     55irodsZone '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 ===
     72In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
     73local 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/GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Analyze Back to previous step]]
     103
     104[[http://groups.geni.net/geni/wiki/GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Cleanup Forward to next step]]
     105
     106[[http://groups.geni.net/geni/wiki/GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/ Back to tutorial main page]]