Difference between revisions of "YH-T-Template"
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| Line 25: | Line 25: | ||
The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END --> | The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END --> | ||
| − | + | Here is an example of a shell script, sub.sh, to run on at the batch queue: | |
| − | < | + | <divp class="gscript"> |
#!/bin/bash | #!/bin/bash | ||
#SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | #SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | ||
| − | #SBATCH --partition= | + | #SBATCH --partition=batch |
#SBATCH --mail-type=ALL | #SBATCH --mail-type=ALL | ||
| − | #SBATCH --mail-user=username@uga.edu | + | #SBATCH --mail-user=<u>username@uga.edu</u> |
| − | #SBATCH --ntasks=1 | + | #SBATCH --ntasks=<u>1</u> |
| − | #SBATCH --mem=10gb | + | #SBATCH --mem=<u>10gb</u> |
| − | #SBATCH --time=08:00:00 | + | #SBATCH --time=<u>08:00:00</u> |
#SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out | #SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out | ||
| Line 40: | Line 40: | ||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
| − | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] | + | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u> |
</p> | </p> | ||
Revision as of 21:50, 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: <divp class="gscript">
- !/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