YH-T-Template

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

To use this version, please first load the module with

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

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

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

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

#!/bin/bash
#SBATCH --job-name=j_trinity
#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=trinity.%j.out

cd $SLURM_SUBMIT_DIR

ml [options]

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

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

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Installation

Source code is obtained from Trinity

System

64-bit Linux