| 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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| 25 | </map> |
| 26 | <!-- Image map text links - End - --> |
| 27 | |
| 28 | </div> |
| 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]] |