1 | | == F. Pull from iRODS == |
2 | | |
3 | | {{{ |
4 | | #!html |
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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]] |