ICommands-Sapelo2 - Revision history

Shtsai at 00:49, 5 April 2026

2026-04-05T00:49:32Z

← Older revision		Revision as of 20:49, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]		[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

	=== Category ===		== Category ==

	Tools		Tools

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	4.2.8		4.2.8

	=== Author / Distributor ===		== Author / Distributor ==

	Please see [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]		Please see [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]

	=== Description ===		== Description ==

	From [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]: "iCommands is a collection of commands for Linux and Mac OS operating systems that are used in the iRODS system to interact with the CyVerse Data Store."		From [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]: "iCommands is a collection of commands for Linux and Mac OS operating systems that are used in the iRODS system to interact with the CyVerse Data Store."

	=== Running Program ===		== Running Program ==

	Also refer to [[Transferring Files]].		Also refer to [[Transferring Files]].
Line 50:		Line 50:
	If the login succeeds and connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.		If the login succeeds and connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.

	=== Documentation ===		== Documentation ==

	Please see [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]		Please see [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]
Line 56:		Line 56:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Installed on Sapelo2 transfer node xfer-irods.gacrc.uga.edu		Installed on Sapelo2 transfer node xfer-irods.gacrc.uga.edu

	=== System ===		== System ==

	64-bit Linux		64-bit Linux

Shtsai at 15:08, 12 January 2021

2021-01-12T15:08:34Z

← Older revision		Revision as of 11:08, 12 January 2021
Line 11:		Line 11:
	=== Version ===		=== Version ===

	4.1.12		4.2.8

	=== Author / Distributor ===		=== Author / Distributor ===
Line 25:		Line 25:
	Also refer to [[Transferring Files]].		Also refer to [[Transferring Files]].

	* version 4.1.12 is installed on Sapelo2 '''transfer ~~nodes~~''' (xfer.gacrc.uga.edu).		* version 4.2.8 is installed on Sapelo2 IRODS '''transfer node''' (xfer-irods.gacrc.uga.edu). Please note that this command is not available on the other transfer nodes.

	Please log on a Sapelo2 transfer node to use iCommands, for example:		Please log on a Sapelo2 transfer node xfer-irods.gacrc.uga.edu to use iCommands, for example:

	<pre class="gscript">		<pre class="gscript">
	ssh username@xfer.gacrc.uga.edu		ssh username@xfer-irods.gacrc.uga.edu
	</pre>		</pre>

	Once you logged on a transfer node, you can initialize and start the connection to iRODS by iinit command, for example:		Once you logged on this specific transfer node, you can initialize and start the connection to iRODS by using the iinit command, for example:

	<pre class="gscript">		<pre class="gscript">
Line 58:		Line 58:
	=== Installation ===		=== Installation ===

	Installed on Sapelo2 transfer ~~nodes~~		Installed on Sapelo2 transfer node xfer-irods.gacrc.uga.edu

	=== System ===		=== System ===

	64-bit Linux		64-bit Linux

Shtsai at 16:11, 8 December 2020

2020-12-08T16:11:33Z

← Older revision		Revision as of 12:11, 8 December 2020
Line 1:		Line 1:
	[[Category:~~Sapelo2old~~]][[Category:Software]][[Category:Tools]]		[[Category:Sapelo2]][[Category:Software]][[Category:Tools]]

	=== Category ===		=== Category ===

Moses: /* Running Program */

2020-12-08T16:11:18Z

Running Program

← Older revision		Revision as of 12:11, 8 December 2020
Line 25:		Line 25:
	Also refer to [[Transferring Files]].		Also refer to [[Transferring Files]].

	* version 4.1.12 is installed on Sapelo2 transfer nodes ('''xfer.gacrc.uga.edu~~'''~~).		* version 4.1.12 is installed on Sapelo2 '''transfer nodes''' (xfer.gacrc.uga.edu).

	Please log on a Sapelo2 transfer node to use iCommands, for example:		Please log on a Sapelo2 transfer node to use iCommands, for example:

Moses: /* Running Program */

2020-12-08T16:09:54Z

Running Program

← Older revision		Revision as of 12:09, 8 December 2020
Line 25:		Line 25:
	Also refer to [[Transferring Files]].		Also refer to [[Transferring Files]].

	* version 4.1.12 is installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu).		* version 4.1.12 is installed on Sapelo2 transfer nodes ('''xfer.gacrc.uga.edu''').

	Please log on a Sapelo2 transfer node to use iCommands, for example:		Please log on a Sapelo2 transfer node to use iCommands, for example:

Moses: /* Running Program */

2020-12-08T16:08:25Z

Running Program

← Older revision		Revision as of 12:08, 8 December 2020
Line 45:		Line 45:
	Enter your current iRODS password: [yourIRodsPassword]		Enter your current iRODS password: [yourIRodsPassword]
	</pre>		</pre>

			Please replace [yourIRodsUserName], [yourIRodsZone], and [yourIRodsPassword] with your own IRods username, zone name, and login password.

	If the login succeeds and connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.		If the login succeeds and connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.

Moses: /* Running Program */

2020-12-08T16:04:13Z

Running Program

← Older revision		Revision as of 12:04, 8 December 2020
Line 42:		Line 42:
	Enter the port number: 1247		Enter the port number: 1247
	Enter your irods user name: [yourIRodsUserName]		Enter your irods user name: [yourIRodsUserName]
			Enter your irods zone: [yourIRodsZone]
			Enter your current iRODS password: [yourIRodsPassword]
	</pre>		</pre>

	~~Once~~ connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.		If the login succeeds and connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.

	=== Documentation ===		=== Documentation ===

Moses: /* Running Program */

2020-12-08T16:01:47Z

Running Program

← Older revision		Revision as of 12:01, 8 December 2020
Line 25:		Line 25:
	Also refer to [[Transferring Files]].		Also refer to [[Transferring Files]].

	*~~Version~~ 4.1.12 is installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu).		* version 4.1.12 is installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu).

	Please log on a Sapelo2 transfer node to use iCommands:		Please log on a Sapelo2 transfer node to use iCommands, for example:

	<pre class="gscript">		<pre class="gscript">

Moses at 15:59, 8 December 2020

2020-12-08T15:59:45Z

← Older revision		Revision as of 11:59, 8 December 2020
Line 23:		Line 23:
	=== Running Program ===		=== Running Program ===

	Also refer to [[]].		Also refer to [[Transferring Files]].

	*~~version~~ 4.1.12, installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu)		*Version 4.1.12 is installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu).

	Please log on Sapelo2 ~~cluster~~ transfer node to use iCommands.		Please log on a Sapelo2 transfer node to use iCommands:

	<pre class="gscript">		<pre class="gscript">
Line 33:		Line 33:
	</pre>		</pre>

	~~The blast results for the each of the split group will be in~~ a ~~separate file under the specified output directory. The file name will end in fa.OUT. To gather the blast output~~ you can ~~generally concatenate all~~ the ~~individual outputs. You can use the following~~ command ~~to find and concatenate all the output files.~~		Once you logged on a transfer node, you can initialize and start the connection to iRODS by iinit command, for example:

	<pre class="~~gcommand~~">		<pre class="gscript">
	~~find OUTPUT_DIR -~~name '*.fa.~~OUT' \| xargs cat > combined_blast_results.out~~		iinit
			One or more fields in your iRODS environment file (irods_environment.json) are
			missing; please enter them.
			Enter the host name (DNS) of the server to connect to: data.cyverse.org
			Enter the port number: 1247
			Enter your irods user name: [yourIRodsUserName]
	</pre>		</pre>

			Once connection is built, you can use other iCommands, like iget/iput, etc., to download/upload the file/directory between iRODS and your current working directory on the cluster.

	=== Documentation ===		=== Documentation ===

	Please see ~~http~~://~~hpcgridrunner~~.~~github~~.io/		Please see [https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869855/Using+iCommands iCommands]

	[[#top\|Back to Top]]		[[#top\|Back to Top]]
Line 47:		Line 54:
	=== Installation ===		=== Installation ===

	Installed ~~in /apps/eb/HpcGridRunner/1.0.2~~		Installed on Sapelo2 transfer nodes

	=== System ===		=== System ===

	64-bit Linux		64-bit Linux

Moses at 15:43, 8 December 2020

2020-12-08T15:43:02Z

← Older revision		Revision as of 11:43, 8 December 2020
Line 23:		Line 23:
	=== Running Program ===		=== Running Program ===

	~~https://wiki~~.~~gacrc.uga.edu/wiki/Transferring_Files~~		Also refer to [[]].

	*version 4.1.12, installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu)		*version 4.1.12, installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu)