SweStore/iRODS icommand - Revision history

Niklas Edmundsson (HPC2N): Swestore iRODS is decomissioned

2023-02-08T10:14:40Z

Swestore iRODS is decomissioned

Dejan Vitlacil (C3SE) at 06:06, 15 September 2019

2019-09-15T06:06:41Z

Dejan Vitlacil (C3SE) at 08:52, 6 December 2013

2013-12-06T08:52:29Z

Dejan Vitlacil (C3SE) at 08:48, 6 December 2013

2013-12-06T08:48:42Z

Dejan Vitlacil (C3SE) at 08:45, 6 December 2013

2013-12-06T08:45:38Z

Dejan Vitlacil (C3SE) at 08:45, 6 December 2013

2013-12-06T08:45:07Z

Dejan Vitlacil (C3SE) at 08:44, 6 December 2013

2013-12-06T08:44:40Z

Dejan Vitlacil (C3SE) at 08:44, 6 December 2013

2013-12-06T08:44:09Z

Dejan Vitlacil (C3SE) at 08:42, 6 December 2013

2013-12-06T08:42:45Z

Tom Langborg (NSC) at 11:59, 31 October 2013

2013-10-31T11:59:34Z

← Older revision		Revision as of 10:14, 8 February 2023
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−	~~<span style="color:~~#~~FF0000"> NOTA: THIS PAGE IS OUT OF DATE! IT WILL BE SOON DELETED. </span><br>~~	+	#REDIRECT[[Swestore iRODS is decommissioned]]
−
−	~~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".~~
−
−	~~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"~~

← Older revision		Revision as of 06:06, 15 September 2019
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		+	<span style="color:#FF0000"> NOTA: THIS PAGE IS OUT OF DATE! IT WILL BE SOON DELETED. </span><br>
		+
	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".		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".

@@ Line 8: / Line 8: @@
      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:
+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:

← Older revision		Revision as of 08:48, 6 December 2013
Line 1:		Line 1:
−	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".	+	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".

	The iRODS icommands client is loaded through the module system.		The iRODS icommands client is loaded through the module system.

← Older revision		Revision as of 08:45, 6 December 2013
Line 1:		Line 1:
−	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".	+	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".

	The iRODS icommands client is loaded through the module system.		The iRODS icommands client is loaded through the module system.

@@ Line 3: / Line 3: @@
 The iRODS icommands client is loaded through the module system.
-. Log in to SNIC cluster<br>
+. Log in to SNIC cluster
 . Execute:
-     module load irods <br>
+     module load irods
-     iinit <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:

← Older revision		Revision as of 08:42, 6 December 2013
Line 1:		Line 1:
−	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).~~	+	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".
−
−	~~Note that data put on Swestore via iRODS is not accessible through other means~~.

	Activate the iRODS icommands		Activate the iRODS icommands