ICommands-Sapelo2: Difference between revisions

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=== 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">
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</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]]
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=== Installation ===
=== Installation ===


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


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


64-bit Linux
64-bit Linux

Revision as of 10:59, 8 December 2020


Category

Tools

Program On

Sapelo2

Version

4.1.12

Author / Distributor

Please see iCommands

Description

From 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

Also refer to Transferring Files.

  • Version 4.1.12 is installed on Sapelo2 transfer nodes (xfer.gacrc.uga.edu).

Please log on a Sapelo2 transfer node to use iCommands: 

ssh username@xfer.gacrc.uga.edu

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

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]

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

Please see iCommands

Back to Top

Installation

Installed on Sapelo2 transfer nodes

System

64-bit Linux

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