YH-T-Template: Difference between revisions
No edit summary |
No edit summary |
||
| (18 intermediate revisions by the same user not shown) | |||
| Line 21: | Line 21: | ||
=== Running Program === | === Running Program === | ||
The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END --> | |||
To use this version, please load the module with | |||
<pre class="gscript"> | |||
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --> | |||
</pre> | |||
Here is an example of a shell script, sub.sh, to run on the batch queue: | |||
<div class="gscript2"> | |||
<nowiki>#</nowiki>!/bin/bash<br> | |||
<nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br> | |||
<nowiki>#</nowiki>SBATCH --partition=batch<br> | |||
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | |||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | |||
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> | |||
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> | |||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | |||
<nowiki>#</nowiki>SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out<br> | |||
<nowiki>#</nowiki>SBATCH --error=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | |||
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --><br> | |||
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u><br> | |||
</div> | |||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | |||
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | |||
# | |||
# | |||
Here is an example of job submission command: | Here is an example of job submission command: | ||
| Line 51: | Line 59: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
<!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END --> | ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --> | ||
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END --> | |||
</pre> | </pre> | ||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
Latest revision as of 12:59, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.0.6
Author / Distributor
Trinity
Description
"" More details are at Trinity
Running Program
The last version of this application is at trinity
To use this version, please load the module with
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END -->
Here is an example of a shell script, sub.sh, to run on 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
#SBATCH --error=trinity.%j.err
cd $SLURM_SUBMIT_DIR
ml
[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.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --> <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->
Installation
Source code is obtained from Trinity
System
64-bit Linux