Difference between revisions of "YH-T-Template"
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<div class="gscript"> | <div class="gscript"> | ||
<nowiki>#</nowiki>!/bin/bash | <nowiki>#</nowiki>!/bin/bash | ||
| − | <nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | + | |
| − | <nowiki>#</nowiki>SBATCH --partition=batch | + | <nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> |
| − | <nowiki>#</nowiki>SBATCH --mail-type=ALL | + | |
| + | <nowiki>#</nowiki>SBATCH --partition=batch | ||
| + | |||
| + | <nowiki>#</nowiki>SBATCH --mail-type=ALL | ||
| + | |||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u> | <nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u> | ||
| − | <nowiki>#</nowiki>SBATCH --ntasks=<u>1</u> | + | |
| − | <nowiki>#</nowiki>SBATCH --mem=<u>10gb</u> | + | <nowiki>#</nowiki>SBATCH --ntasks=<u>1</u> |
| − | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</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 | <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 --> <u>[options]</u> | ||
</div> | </div> | ||
Revision as of 21:56, 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_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
cd $PBS_O_WORKDIR
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