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=== Running Program === | === Running Program === | ||
The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END --> | |||
<pre class="gscript"> | |||
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> | |||
</pre> | |||
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"> | ||
#PBS -S /bin/bash | <nowiki>#</nowiki>PBS -S /bin/bash | ||
#PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | <nowiki>#</nowiki>PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | ||
#PBS -q batch | <nowiki>#</nowiki>PBS -q batch | ||
#PBS -l nodes=1:ppn=1:AMD | <nowiki>#</nowiki>PBS -l nodes=<u>1</u>:ppn=<u>1</u>:<u>AMD</u> | ||
#PBS -l walltime= | <nowiki>#</nowiki>PBS -l walltime=<u>8:00:00</u> | ||
#PBS -l mem=10gb | <nowiki>#</nowiki>PBS -l mem=<u>10gb</u> | ||
<nowiki>#</nowiki>PBS -M <u>username@uga.edu</u> | |||
<nowiki>#</nowiki>PBS -m abe | |||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] | <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] | ||
</ | </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 or be reviewed . | |||
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 command: | Here is an example of job submission command: | ||
Revision as of 11:22, 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