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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).
| + | #REDIRECT[[Swestore iRODS is decommissioned]] |
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| − | Note that data put on Swestore via iRODS is not accessible through other means.
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| − | Activate the iRODS icommands
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| − | The iRODS icommands client is activated through the module system, as so many other things on SNIC clusters.
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| − | 1. Log in to SNIC cluster
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| − | 2. Execute:
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| − | module load irods
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| − | iinit
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| − | 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:
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| − | [samuel@kalkyl4 ~]$ ils
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| − | /ssUppnexZone/proj/b2011221:
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| − | C- /ssUppnexZone/proj/b2011221/firstRun
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| − | Navigate around
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| − | To enter one of the (or the only) folder(s), do:
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| − | icd [proj-id]
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| − | ... in this case:
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| − | icd firstrun
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| − | To switch to another project, use
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| − | icd ..
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| − | to back up a level. After that, you can change to another project or folder using icd as previously
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| − | icd b2011222
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| − | Upload files
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| − | To upload the above mentioned folder, do (-r is needed to recurse into directories):
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| − | iput -r [a local folder]
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| − | For single files, the -r flag is not needed:
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| − | iput [a local file]
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| − | To list the newly uploaded file/directory:
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| − | ils
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| − | To create folders, do:
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| − | imkdir [folder-name]
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| − | If you want to verify the upload outside of iRODS, there's a utility called ssverify.sh that will let you do that.
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| − | $ ssverify.sh test /ssUppnexZone/proj/p2061001/test
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| − | Checking if test/a matches /ssUppnexZone/proj/p2061001/test/a... seems good!
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| − | Checking if test/b matches /ssUppnexZone/proj/p2061001/test/b... seems good!
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| − | Checking if test/c matches /ssUppnexZone/proj/p2061001/test/c... seems good!
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| − | Checking if test/du matches /ssUppnexZone/proj/p2061001/test/du... seems good!
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| − | Checking if test/foo matches /ssUppnexZone/proj/p2061001/test/foo... seems good!
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| − | It seems test matches /ssUppnexZone/proj/p2061001/test on Swestore.
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| − | $ echo femtiofyra > test/c
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| − | $ ssverify.sh test /ssUppnexZone/proj/p2061001/test
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| − | Checking if test/a matches /ssUppnexZone/proj/p2061001/test/a... seems good!
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| − | Checking if test/b matches /ssUppnexZone/proj/p2061001/test/b... seems good!
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| − | Checking if test/c matches /ssUppnexZone/proj/p2061001/test/c... NO! Something is wrong!
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| − | Either the files don't match or something went wrong, please contact
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| − | staff@uppmax.uu.se to investigate.
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| − | Downloading files
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| − | To download a file again, do:
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| − | iget [a file in iRODS]
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| − | ... or, for folders, do it recursively:
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| − | iget -r [a folder in iRODS]
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| − | File removal
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| − | 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.
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| − | More hints
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| − | You can have iput show the progress with the -P flag
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| − | If you want to be placed in a particular directory when you load the irods module, you can create a file called
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| − | $HOME/.irods/.irodsEnv
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| − | containing
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| − | irodsHome '/ssUppnexZone/proj/myproj'
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| − | irodsCwd '/ssUppnexZone/proj/myproj'
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| − | where
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| − | myproj
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| − | is replaced by your project id.
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| − | Read more info about the respective i-commands with "[command] -h"
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