YH-T-Template: Difference between revisions

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Here is an example of a shell script, sub.sh, to run on at the batch queue:  
Here is an example of a shell script, sub.sh, to run on at the batch queue:  
<div class="gscript">
<pre class="gscript">
<nowiki>#</nowiki>!/bin/bash
#!/bin/bash
<nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END -->  
#SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END -->  
     
#SBATCH --partition=batch         
<nowiki>#</nowiki>SBATCH --partition=batch         
#SBATCH --mail-type=ALL  
   
#SBATCH --mail-user=username@uga.edu   
<nowiki>#</nowiki>SBATCH --mail-type=ALL  
#SBATCH --ntasks=1   
       
#SBATCH --mem=10gb     
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u>  
#SBATCH --time=08:00:00   
 
#SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u>    
               
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u>    
               
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u>    
           
<nowiki>#</nowiki>SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out
 
   
cd $SLURM_SUBMIT_DIR
cd $SLURM_SUBMIT_DIR


cd $PBS_O_WORKDIR
cd $PBS_O_WORKDIR


ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u>    
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options]   
</div>  
</pre>


Here is an example of job submission command:
Here is an example of job submission command:

Revision as of 21:01, 6 August 2018

Category

Bioinformatics

Program On

Teaching

Version

2.0.6

Author / Distributor

Trinity

Description

"" More details are at Trinity

Running Program

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for generic details about running jobs at Teaching.

The last version of this application is at trinity

Here is an example of a shell script, sub.sh, to run on at the batch queue: 

#!/bin/bash
#SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> 
#SBATCH --partition=batch        
#SBATCH --mail-type=ALL 
#SBATCH --mail-user=username@uga.edu  
#SBATCH --ntasks=1   
#SBATCH --mem=10gb    
#SBATCH --time=08:00:00   
#SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out
 
cd $SLURM_SUBMIT_DIR

cd $PBS_O_WORKDIR

ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options]

Here is an example of job submission command: 

sbatch ./sub.sh

Documentation

<!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->

Back to Top

Installation

Source code is obtained from Trinity

System

64-bit Linux

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