Difference between revisions of "Icommands"

Latest revision as of 18:39, 15 August 2022

Description

iCommands is a collection of commands for Unix and Windows that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, you use ls in Linux, but in iCommands you use ils.

While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (2-100 GB each) and for bulk file transfers (many small files). For a comparison of the different methods of uploading and downloading data items, see Downloading and Uploading Data.

Using iCommands with your CyVerse username and password allows you access to all files that have been shared by other users; however, you can download data sets that have been made public without a CyVerse account.

Environment Modules

Run module spider icommands to find out what environment modules are available for this application.

System Variables

HPC_ICOMMANDS_DIR - installation directory

Additional Information

Since iCommands binaries are not compatible with our system iCommands binaries have to be launched with the 'launch_icommands' command.

For example:

$ module load icommands
$ launch_icommands ienv -h

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]]
+[[Category:Software]][[Category:Utility]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|icommands}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-iCommands is a collection of commands for Unix and Windows that are used in
+iCommands is a collection of commands for Unix and Windows that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, you use ls in Linux, but in iCommands you use ils.
-the iRODS system to interact with the CyVerse Data Store. Many commands are
-very similar to Unix utilities. For example, to list files and directories,
-you use ls in Linux, but in iCommands you use ils.
-While iCommands are great for all transfers and for automating tasks via
+While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (2-100 GB each) and for bulk file transfers (many small files). For a comparison of the different methods of uploading and downloading data items, see Downloading and Uploading Data.
-scripts, they are the best choice for large files (2-100 GB each) and for
-bulk file transfers (many small files). For a comparison of the different
-methods of uploading and downloading data items, see Downloading and
-Uploading Data.
-Using iCommands with your CyVerse username and password allows you access to
+Using iCommands with your CyVerse username and password allows you access to all files that have been shared by other users; however, you can download data sets that have been made public without a CyVerse account.
-all files that have been shared by other users; however, you can download
-data sets that have been made public without a CyVerse account. Instructions
-for both are below.
 <!--Modules-->
@@ Line 46: / Line 36: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+Since iCommands binaries are not compatible with our system iCommands binaries have to be launched with the 'launch_icommands' command.
+For example:
+ $ module load icommands
+ $ launch_icommands ienv -h
 |}}