Difference between revisions of "SweStore/iRODS icommand"

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(Swestore iRODS is decomissioned)
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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".
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#REDIRECT[[Swestore iRODS is decommissioned]]
 
 
The iRODS icommands client is loaded through the module system.
 
 
 
1. Log in to SNIC cluster
 
2. Execute:
 
    module load irods
 
    iinit
 
 
 
Now, your starting point is either your Swestore home directory or one of your projects. If you run "ils", you will then see a listing of files and folders in that directory, 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