Difference between revisions of "JEX"

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[[Image:JEX Diagram1.png|center|500px|High level diagram illustrating how tools on CoGe have jobs processed.]]<br>
 
[[Image:JEX Diagram1.png|center|500px|High level diagram illustrating how tools on CoGe have jobs processed.]]<br>
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== Summary  ==
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Yerba is the job execution engine used by CoGe. For more details on why the job engine is used by CoGe refer to&nbsp;[http://genomevolution.org/wiki/index.php/JEX Job Execution Framework].
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== Installation ==
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For installation instructions please refer to the [https://github.com/LyonsLab/Yerba/tree/temp git repository] or the README.md in the repository.<br>
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To clone the repository run the command:
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git clone https://github.com/LyonsLab/Yerba.git
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== Usage<br>  ==
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Yerba has two components the job daemon ''yerbad'' and the command line client ''yerba''. The job daemon is started started when the server is first booted. Additionally, cctool's catalog and worker pool need to be running. ''yerba' is a command line interface to the job engine to check the status of the job engine. More features are planned in the future.
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==== yerbad<br>  ====
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To (manually) start the job engine you need to start each script.
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sudo start catalog_server
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sudo start work_queue_pool
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sudo start yerba
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==== yerba ====
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This command currently only checks for a response from the job engine.
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$YERBA_DIR/bin/yerba
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Another method to check the status of the job engine is:
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status yerba
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==  CoGe yerba utilities<br>  ==
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CoGe has several utilities that provide functionality beyond the scope of the job engine.
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==== update_jobs ====
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This script keeps the CoGe jobs table up to date. By default the command will perform a dry run and not update the database.
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coge/scripts/update-jobs coge.conf
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To update the database the command can then be ran with the update argument.
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coge/scripts/update-jobs coge.conf --update

Revision as of 12:11, 26 June 2014

Overview

CoGe is in the process of moving all analysis to the job execution framework. The job execution framework allows analysis to run in a hetrogenous environment. An analysis can then be run in an environment which best suits its computational needs.

High level diagram illustrating how tools on CoGe have jobs processed.

Summary

Yerba is the job execution engine used by CoGe. For more details on why the job engine is used by CoGe refer to Job Execution Framework.

Installation

For installation instructions please refer to the git repository or the README.md in the repository.

To clone the repository run the command: 

git clone https://github.com/LyonsLab/Yerba.git

Usage

Yerba has two components the job daemon yerbad and the command line client yerba. The job daemon is started started when the server is first booted. Additionally, cctool's catalog and worker pool need to be running. yerba' is a command line interface to the job engine to check the status of the job engine. More features are planned in the future.

yerbad

To (manually) start the job engine you need to start each script. 

sudo start catalog_server
sudo start work_queue_pool
sudo start yerba

yerba

This command currently only checks for a response from the job engine. 

$YERBA_DIR/bin/yerba

Another method to check the status of the job engine is: status yerba

CoGe yerba utilities

CoGe has several utilities that provide functionality beyond the scope of the job engine.

update_jobs

This script keeps the CoGe jobs table up to date. By default the command will perform a dry run and not update the database. 

coge/scripts/update-jobs coge.conf

To update the database the command can then be ran with the update argument. 

coge/scripts/update-jobs coge.conf --update
Retrieved from "https://genomevolution.org/wiki/index.php?title=JEX&oldid=6509"