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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="gscript2"> | <div class="gscript2"> | ||
<nowiki>#</nowiki>PBS -S /bin/bash | <nowiki>#</nowiki>PBS -S /bin/bash<br> | ||
<nowiki>#</nowiki>PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | <nowiki>#</nowiki>PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br> | ||
<nowiki>#</nowiki>PBS -q batch | <nowiki>#</nowiki>PBS -q batch<br> | ||
<nowiki>#</nowiki>PBS -l nodes=<u>1</u>:ppn=<u>1</u>:<u>AMD</u> | <nowiki>#</nowiki>PBS -l nodes=<u>1</u>:ppn=<u>1</u>:<u>AMD</u><br> | ||
<nowiki>#</nowiki>PBS -l walltime=<u>8:00:00</u> | <nowiki>#</nowiki>PBS -l walltime=<u>8:00:00</u><br> | ||
<nowiki>#</nowiki>PBS -l mem=<u>10gb</u> | <nowiki>#</nowiki>PBS -l mem=<u>10gb</u><br> | ||
<nowiki>#</nowiki>PBS -M <u>username@uga.edu</u> | <nowiki>#</nowiki>PBS -M <u>username@uga.edu</u><br> | ||
<nowiki>#</nowiki>PBS -m abe | <nowiki>#</nowiki>PBS -m abe<br> | ||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR<br> | ||
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] | <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options]<br> | ||
</div> | </div> | ||
Revision as of 12:22, 8 August 2018
Category
Bioinformatics
Program On
Sapelo2
Version
2.0.6
Author / Distributor
Trinity
Description
"" More details are at Trinity
Running Program
The last version of this application is at trinity
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END -->
Here is an example of a shell script, sub.sh, to run on at the batch queue:
#PBS -S /bin/bash
#PBS -N j_trinity
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=8:00:00
#PBS -l mem=10gb
#PBS -M username@uga.edu
#PBS -m abe
cd $PBS_O_WORKDIR
[options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values or be reviewed .
Please refer to Running Jobs on Sapelo2, Run X window Jobs and Run interactive Jobs for more details about running jobs at Sapelo2.
Here is an example of job submission command:
qsub ./sub.sh
Documentation
<!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->
Installation
Source code is obtained from Trinity
System
64-bit Linux