Difference between revisions of "YH-T-Template"
| Line 51: | Line 51: | ||
<div class="gscript"> | <div class="gscript"> | ||
| − | <nowiki>#</nowiki>!/bin/bash | + | <nowiki>#</nowiki>!/bin/bash<br> |
| − | <nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | + | <nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br> |
| − | <nowiki>#</nowiki>SBATCH --partition=batch | + | <nowiki>#</nowiki>SBATCH --partition=batch<br> |
| − | <nowiki>#</nowiki>SBATCH --mail-type=ALL | + | <nowiki>#</nowiki>SBATCH --mail-type=ALL<br> |
| − | <nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u> | + | <nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> |
| − | <nowiki>#</nowiki>SBATCH --ntasks=<u>1</u> | + | <nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> |
| − | <nowiki>#</nowiki>SBATCH --mem=<u>10gb</u> | + | <nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> |
| − | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u> | + | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> |
| − | <nowiki>#</nowiki>SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out | + | <nowiki>#</nowiki>SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out<br> |
| − | cd $SLURM_SUBMIT_DIR | + | cd $SLURM_SUBMIT_DIR<br> |
| − | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u> | + | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u><br> |
</div> | </div> | ||
Revision as of 10:13, 7 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
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 -->
Installation
Source code is obtained from Trinity
System
64-bit Linux