Difference between revisions of "YH-T-Template"
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| Line 27: | Line 27: | ||
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"> | <pre class="gscript"> | ||
| − | # | + | #!/bin/bash |
| − | # | + | #SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> |
| − | # | + | #SBATCH --partition=batch |
| − | # | + | #SBATCH --mail-type=AIL |
| − | # | + | #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 | cd $PBS_O_WORKDIR | ||
| Line 40: | Line 45: | ||
Here is an example of job submission command: | Here is an example of job submission command: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
| − | + | sbatch ./sub.sh | |
</pre> | </pre> | ||
Revision as of 12:54, 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 Teaching, 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=AIL
#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
<!-- 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