YH-S2-Template: Difference between revisions
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=== 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>PBS -S /bin/bash<br> | |||
<nowiki>#</nowiki>PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br> | |||
<nowiki>#</nowiki>PBS -q batch<br> | |||
<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><br> | |||
<nowiki>#</nowiki>PBS -l mem=<u>10gb</u><br> | |||
<nowiki>#</nowiki>PBS -M <u>username@uga.edu</u><br> | |||
<nowiki>#</nowiki>PBS -m abe<br> | |||
cd $PBS_O_WORKDIR<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 Sapelo2]], [[Running_Jobs_on_Sapelo2#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_Sapelo2#Running_an_Interactive_Job | Run interactive Jobs]] for more details about running jobs at Sapelo2. | |||
# | |||
# | |||
Here is an example of job submission | Here is an example of job submission command: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
qsub ./sub.sh | qsub ./sub.sh | ||
| Line 48: | Line 58: | ||
<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]] | ||
| Line 54: | Line 65: | ||
=== Installation === | === Installation === | ||
Source code is obtained from <!-- ARCHIVE_URL BEGIN --> [http://trinityrnaseq.sourceforge.net/ Trinity] <!-- ARCHIVE_URL END --> | |||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 12:12, 10 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
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:
#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
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 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
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