Difference between revisions of "YH-T-Template"
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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: | ||
| − | < | + | <pre class="gscript"> |
| − | + | #!/bin/bash | |
| − | + | #SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | |
| − | + | #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=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out | |
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cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
| − | |||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
| − | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END -- | + | ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] |
| − | </ | + | </pre> |
Here is an example of job submission command: | Here is an example of job submission command: | ||
Revision as of 22:01, 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_<!-- NAME BEGIN -->trinity<!-- NAME END --> #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=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out cd $SLURM_SUBMIT_DIR cd $PBS_O_WORKDIR ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [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