Difference between revisions of "SweStore/iRODS icommand"

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For accessing the Swestore national storage, we use (since Nov 2013 iRODS, and more specifically the iRODS client called "icommands", which is a set of commands similar to the unix commands "ls", "cd", "imkdir" etc, but with an "i" in front, plus two FTP-like commands: "iput" and "iget" (plus some more, but those are the ones you need most).
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#REDIRECT[[Swestore iRODS is decommissioned]]
 
 
Note that data put on Swestore via iRODS is not accessible through other means.
 
 
 
Activate the iRODS icommands
 
The iRODS icommands client is activated through the module system, as so many other things on SNIC clusters.
 
 
 
1. Log in to SNIC cluster<br>
 
2. Execute:
 
 
 
module load irods <br>
 
iinit
 
After activating the iRODS icommands, you will be placed in one of your projects. if you run "ils", you will then see a listing of files and folders in that project, something like this:
 
 
 
[samuel@kalkyl4 ~]$ ils
 
  /ssUppnexZone/proj/b2011221:
 
    C- /ssUppnexZone/proj/b2011221/firstRun
 
Navigate around
 
To enter one of the (or the only) folder(s), do:
 
 
 
icd [proj-id]
 
... in this case:
 
 
 
icd firstrun
 
To switch to another project, use
 
 
 
icd ..
 
to back up a level. After that, you can change to another project or folder using icd as previously
 
 
 
icd b2011222
 
Upload files
 
To upload the above mentioned folder, do (-r is needed to recurse into directories):
 
 
 
iput -r [a local folder]
 
For single files, the -r flag is not needed:
 
 
 
iput [a local file]
 
To list the newly uploaded file/directory:
 
 
 
ils
 
To create folders, do:
 
 
 
imkdir [folder-name]
 
If you want to verify the upload outside of iRODS, there's a utility called ssverify.sh that will let you do that.
 
 
 
Downloading files
 
To download a file again, do:
 
 
 
iget [a file in iRODS]
 
... or, for folders, do it recursively:
 
 
 
iget -r [a folder in iRODS]
 
File removal
 
To remove a file, you'll like need to use -f to irm in order to bypass the use of a trash area, which is currently not supported at Uppmax.
 
 
 
More hints
 
You can have iput show the progress with the -P flag
 
If you want to be placed in a particular directory when you load the irods module, you can create a file called
 
$HOME/.irods/.irodsEnv
 
containing
 
irodsHome '/ssUppnexZone/proj/myproj'
 
irodsCwd '/ssUppnexZone/proj/myproj'
 
where
 
myproj
 
is replaced by your project id.
 
Read more info about the respective i-commands with "[command] -h"
 

Latest revision as of 10:14, 8 February 2023